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Chapter 2 THE CHEMISTRY OF LIFE California State Standards 1h: most macromolecules in cells and organisms are synthesized from a small collection of simple precursor 4e: proteins can differ from one another in the number and sequence of amino acids 1b: enzymes are proteins that catalyze biochemical reactions without altering the reactions equilibrium and the activities of enzymes depend on the temperature, ionic conditions, and the pH of the surroundings CHAPTER 2: THE CHEMISTRY OF LIFE The first job of a biologist is to understand the chemistry of life. 2-1 The Nature of Matter A. Atoms Atoms ___________= the basic unit of matter (has volume and mass; solid, liquid, gas, and plasma) Atoms are made subatomic particles called protons, neutrons, and electrons Carbon Atom = - = protons - Positively charged - 1 amu = neutrons - No charge - 1 amu - electrons Electronegative charge 1/1840 amu electrons travel in regions outside the nucleus called orbitals Nucleus _______________= center of an atom. Home to protons and neutrons. B B. Elements Elements= pure substances that consists entirely of one type of atom 100 More than _____known kinds; 2 dozen are common in living organisms Found on the Periodic table Reading the Periodic Table Example: The element Carbon (only made of carbon atoms) An Element in the Periodic Table Atomic number = Number of protons in an atom; different for each element Section 2-1 SYMBOL ____________ usually 1-2 letters _______________= MASS NUMBER # Protons + # neutrons in an atom; the average of one elements isotopes 6 C Carbon 12.011 ____________ NAME of the element Isotopes are the various forms of an atom that differ based on the number of neutrons in the nucleus such as C 14. The isotopes that differ from the most common form are often radioactive or unstable. C. Chemical Compounds 1. Chemical compound= a substance formed by the combination of 2 or more elements in definite proportions. Example: Sodium Chloride = Table salt Forms when sodium and chlorine combine in a 1:1 ratio 2. Chemical formula= a short hand that shows chemical composition Example: Sodium Chloride= NaCl Chemical properties 3. ____________________________ of a molecule Example: NaCl = white crystalline solid Na = a soft silvery metal that reacts explosively with water Cl = poisonous greenish gas D. Chemical Bonds • Atoms in compounds are held together by links called chemical bonds. • Involves the interaction of electrons • covalent and _________ ionic 2 main types of bonds are: ___________ 1. Ionic Bonds a. are formed by the transfer of one or more electrons from one atom to another. b. ion= an atom that has a positive or negative charge as a result of gaining or losing electrons. FORMING AN IONIC BOND Figure 2 -3 Ionic Bonding Section 2 -1 Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na +) Chloride ion (Cl -) Transfer of electron Protons +11 Electrons -11 Charge Protons +17 Electrons -17 Charge 0 0 Protons +11 Electrons -10 Charge +1 c. Opposite charges attract creating a bond between the ions Protons +17 Electrons -18 Charge -1 2. Covalent Bonds a. formed by the sharing of electrons between 2 atoms. b. Sharing means that the moving electrons are actually traveling in the orbitals of both atoms. c. atoms sharing 2 electrons= single bond __ 4 electrons=double bond 6 electrons= triple bond d. _________________= The smallest unit of Molecule most chemical compounds (those joined with covalent bonds) 2-2 What property of water explains why this insect can stand on water? Why does ice float? Ice is less dense than water. Solid (Ice) Liquid (water) Gas (water vapor) Water is Polar—uneven distribution of electrons Hydrogen bonds Water Cohesion & Adhesion Water properties http://www.uni.edu/~iowawet/H2OProperties.html http://www.ccs.k12.in.us/chsBS/kons/kons/physical_properties_of_water.htm Solution Water has a pH of 7 which means that [H+] = [OH-] Acids contain higher concentrations of [H+] ions than water. Bases contain lower concentrations of [H+] ions than water. 2-2 Properties of Water- Refer to reader’s guide 2-3 Carbon Compounds A. The Chemistry of Carbon valence electrons which means 1. Carbon has 4 ________________ covalent bonds. carbon can form 4 _________________ 2. Living organisms are made up of molecules that consist of carbon, hydrogen, oxygen, phosphorus, nitrogen and sulfur. 3. Carbon can bond with itself forming chains of unlimited and form, rings, and complex Figurelength 2-11 Carbon Compounds structures. Section 2-3 Methane Acetylene Butadiene Benzene Isooctane B. Macromolecules 1. Macromolecules= are giant molecules consisting of 1000+ smaller molecules. 2. Polymerization= process of joining small molecules to form large molecules 3. Monomers= small units that form polymers (large molecules) 4. The _____ 4 groups of organic compounds found in living things are: • carbohydrates • lipids • nucleic acids • proteins Polymerization http://www.uwsp.edu/chemistry/tzamis/additionpolymer.html Made of Carbohydrate C,H,O 1:2:1 Example Glucose C6H12O6 Function 1.Stores Energy -animals = GLYCOGEN Monomer Monosaccharide = SINGLE SUGAR -plants = STARCH Mono + mono 2. Structural +mono= Purposes - PLANT CELL POLYSACCHARIDE WALLS (CELLULOSE) - CHITIN (INSECT EXOSKELETON) Lipids Mostly C, H Very little O 1. FATS OILS WAXES 2. STEROIDS Stores Energy Form cell membranes 3. Waterproof coverings 4. Chemical messengers 1 glycerol 3 fatty acids SaturatedNO DOUBLE BONDS IN FATTY ACID UnsaturatedAT LEAST ONE DOUBLE BOND Challenge Question Why are most unsaturated fats liquid at room temperature? • Unsaturated Made of Nucleic acids C H O P N Example Function DNA/RNA Stores and transmits hereditary information Monomer Nucleotide= 1. 5-C SUGAR 2. PHOSPHATE GROUP 3. NITROGENOUS BASE Proteins C H O N methionine Shape determines function 1.HELPS CONTROL RATE OF REACTIONS (ENZYMES) 2. pump small molecules in and out of the cell 3. aids in cell movement Amino acids 20 KINDS Carbohydrates Lipids Nucleic acids • Nucleic acids are polymers of nucleotides joined together to make large macromolecules. • The important nucleic acids are deoxyribonucleic acid(DNA) and various types of ribonucleic acids(RNA). Proteins • Protein are the building blocks of our body. We find protein in our bones, and muscles. We find protein in our hair and nails. There is protein in our brain, and also protein is part of our blood. Summary http://www.chemistryland.com/ElementarySchool/BuildingBlocks/BuildingOrganic.htm Concept Summary Concept Map Choose from the following: lipids, nucleotides, amino acids, fats and oils, Carbohydreat sugars and starches, carbohydrates, nucleic acids, proteins Carbon Compounds include Carbohydrates Lipids Nucleic acids Proteins that consist of that consist of that consist of that consist of Sugars and starches Fats and oils Nucleotides Amino Acids which contain which contain Carbon, hydrogen, oxygen Carbon, hydrogen, oxygen which contain which contain Carbon,hydrogen, oxygen, nitrogen, phosphorus Carbon, hydrogen,oxygen, nitrogen, IQ Quiz: Chapter 2 1. 2. 3. 4. What kind of compounds did we test in the lab? What chemical was used to test for simple sugars? What was a positive result? If we want to see if peanuts have fat in them what could we do? 5. How do we know if it is positive? 6. What did copper sulfate and sodium hydroxide test for? 7. What was a positive result? 8. If I had a bowl of cereal and Iodine fell into my cereal and turned a blue-black color what do I know is in my cereal? 9. Name a food that had more than 1 compound in it? (tested positive for more than 1 test) 10. What are the four most common elements in living things? 2-4 Chemical Reactions and Enzymes A. Chemical Reactions =process that changes, or transforms one set of chemicals into another. Always involves changes in chemical bonds. 1. Reactants= elements or compounds that enter a reaction 2. Products= elements or compounds produced by a reaction EXAMPLE: HCl H + Cl B. Energy in Reactions • Activation Energy= energy that is needed to get a reaction started C. Enzymes 1. Catalyst= a substance that speeds up the rate of a chemical reaction without changing itself. 2. Catalysts ___________________________in a chemical reaction. lower the activation energy Reaction with no enzyme AE without enzyme AE with enzyme reactants Reaction with an enzyme products 3. ______________ are ___________________ Enzymes biological catalysts that speed up favorable (spontaneous) reactions. speed up chemical reactions that 4. Enzymes _____________ take place in cells. 5. Enzymes are very specific D. Enzyme Action 1. The Enzyme-Substrate Complex a. Enzymes provide a site where reactants can be brought together to react (increasing the rate of reaction by reducing the activation energy) Figure 2 -21 Enzyme Action Enzyme Activity Section 2 -4 Active site= Site on the enzyme where the substrate attaches Enzyme (hexokinase) Glucose Substrates Products ADP Glucose -6phosphate ATP Products are released The reactants of a catalyzed reaction Substrates bind to enzyme Substrates are converted into products Enzymesubstrate complex b. Enzymes are not consumed in the reaction; after products are formed, the enzyme is recycled. 2. Regulation of Enzyme Activity - Enzyme activity depends on environmental factors such as: pH (enzymes in the stomach function best around pH=2) temperature (human enzymes function best around 37°C) -Ionic conditions (coenzymes) -Substrate concentration (greater the concentration the greater the rate of the reaction) http://www.kscience.co.uk/animations/model.swf http://www.lewport.wnyric.org/JWANAMAKER/animations/Enzyme%20activity.html Warm-up questions 1. Describe the difference between ionic and covalent bonds. Provide an example for each. Warm-up 1. What are the 4 organic macromolecules which make up living organisms. 2. What are the monomers (building blocks) to these macromolecules. Warm-up 1. What is a catalyst? 2. What are enzymes? 3. How do catalyst work? 4. What affects the activity of an enzyme? Review 1. The positively charged particle in an atom is the a. Neutron Ion Proton electron b. c. d. Review 2. a. b. c. d. Two or more different atoms are combined in definite proportions in any Symbol Isotope Element Compound Review 3. A covalent bond is formed by the a. Transfer of electrons Sharing of electrons Gaining of electrons Losing of electrons b. c. d. Review 4. When you shake sugar and sand together in a test tube, you cause them to form a a. Compound Mixture Solution suspension b. c. d. Review 5. A compound that produces hydrogen ions in solution is a. Salt Acid Base polymer b. c. d. Review 6. In polymerization, complex molecules are formed by the joining together of a. Macromolecules Carbohydrates Polymers monomers b. c. d. Review 8. Proteins are polymers formed from a. Lipids Carbohydrates Amino acids Nucleic acids b. c. d. Review 9. An enzyme speeds up a reaction by a. b. c. d. Lowering activation energy Raising activation energy Releasing energy Absorbing energy Review 10. In a chemical reaction, a reactant binds to an enzyme at a region known as the a. Catalyst Product Substrate Active site b. c. d. Standardized Test Prep 1. 2. 3. An attraction between different substances Lower a chemical reaction’s activation energy The elements or compounds that enter into a chemical reaction Choose: Cohesion Adhesion Catalysts Reactants Products STP 4. a. b. c. d. e. Which one of the following is NOT an organic molecule found in living organisms Protein Nucleic acid Carbohydrate Sodium chloride lipid STP 5. a. b. c. d. e. Which combination of particle and charge is correct? Proton: + Electron: + Neutron: Proton: Electron: 0 STP 6. In which of the following ways do isotopes of the same element differ? a. # neutrons only #protons only #neutrons and protons #protons and mass #neutrons and mass b. c. d. e. STP 7. a. b. c. d. e. Which of the following molecules is made up of glycerol and fatty acids? Sugars Starches Lipids Nucleic acids Proteins STP 8. Nucleotides consist of a phosphate group, a nitrogenous base, and a a. Fatty acid Starch Lipid 5 carbon sugar 6 carbon sugar b. c. d. e.