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Biology Chapter 2 The Chemistry of Life I. The nature of matterA. Atoms-_____________ Derived from Greek word Atomos,which means “unable to be cut” As described by _____________________,2300 years ago Basic unit of matter Democritus Atoms cont’d 100 million atoms would make a room about 1 cm long DOES contain__________________particles that are smaller than an atom subatomic Subatomic particles particle size location electron 1/1840th mass Energy of a levels in an amu(proton) electron proton 1 amu cloud nucleus neutron 1amu nucleus charge - + none Calculating subatomic particles: PROTONS=Atomic Number=electrons(in a neutral atom) MASS NUMBER=p + n N=Mass-p Electrons=p=atomic number Examples: For Cl –atomic # =17 and mass =35 P=17,electrons=17,neutrons =35-17=18 For Li---It has 3 protons and 4 neutrons Li has mass number=7 ,atomic # =3 and electrons= 3 Atoms cont’d Since atoms tend to have p=electrons ,the + and – charge balance ,making them neutral _________________center of atom bound by STRONG FORCES. Electrons are attracted to + nucleus ,but are held in levels by the energy of their motion nucleus B. Elements and Isotopes _______________=PURE SUBSTANCE CONSISTING OF ONE KIND OF ATOM More than 100 in existence but ~24 compose living things Represented by 1 or 2 letter symbol Element Common symbols name hydrogen helium lithium boron carbon nitrogen oxygen sym bol H He Li B C N O name symbol Fluorine neon sodium magnesium aluminum Silicon Chlorine F Ne Na Mg Al Si Cl Common symbols name potassium calcium arsenic bromine radon silver gold symbol K Ca As Br Rn Ag Au name mercury tin iodine barium radium phosphorus Uranium symbol Hg Sn I Ba Ra P U Isotopes-atoms of the same element with a different number of neutrons----example:C-12,C-13,C-14----all averaged together for the atomic mass Isotopes are identified by ____________________. Radioactive Isotopes have unstable nuclei and break down at a constant rate over time… Radioactive Isotopes uses:________________________________________ All isotopes of an element have the same chemical properties because they have the same # of ______________-. Mass number Tracers-esp. in medical diagnosis,dating fossils,identifying and treating cancer,kill bacteria electrons Isotopes cont’d ‘WEIGHTED MASS”-ie .Atomic weight=average mass of all isotopes for an element C. Chemical Compounds=_______________________ Shown by a chemical formula Physical and chemical properties for an element differ a lot when they are bound in a compound What is the ratio of H:O on H2O?_________ Substance formed by 2 or more substances in definite proportions 2:1 Physical properties:______________________ Chemical properties:_______________ Don’t change substance— color,smell.. Change substanceflammability ,corrosion D. Chemical Bonds hold together atoms in a compound Ionic Bonds-electrons are transferred from one to another creating an electrical ,ionic charge that binds the atoms Tends to happen between metals and nonmetals Looking @ p.37 ,draw what happens in a NaCl 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 0 Go to Section: Protons +17 Electrons -17 Charge 0 Protons +11 Electrons -10 Charge +1 Protons +17 Electrons -18 Charge -1 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 0 Go to Section: Protons +17 Electrons -17 Charge 0 Protons +11 Electrons -10 Charge +1 Protons +17 Electrons -18 Charge -1 Covalent Bonds-_____________________ The moving electrons of both atoms travel in the orbits of both atoms Double or triple bonds occur when 4 or 6 electrons are shared ______________-smallest unit of a compound See drawing 2-4 on p.37and draw the bond of H2O molecule Share electrons E. Van der Waals Forces_intermolecular forces that result from unequal sharing that results in tiny + or – charges in covalent bonds Help hold a molecule together a little more….see example of gecko on p.39 •Rapid movement of electrons can create regions of tiny (+) and (-) charges/As some molecules are close together,slight attra Rapid movement of electrons can create regions of tiny (+) and (-) charges/As some molecules are close together,slight attraction between oppositely charged regions of nearby molecule-esp. when molecule is large II. Properties of water Single most abundant compound in most living things A. The Water Molecule _____________-because of an uneven distribution of electrons between O and H atoms O side is more – pole because it has more electrons It is ,essentially ,neutral ,but has a more – and more + end Because of this polarity water molecules can attract one another Polar Polar charges are written in ( ) to show they are weaker than ionic charges H bonds not strong ,but water can form___________ H bonds…..causing many of its properties-/bonding with itself O,N, and F multiple A single water molecule can be involved in as many as 4 H-bonds __________________attraction between molecules of the same substance…water is cohesive Cohesion cohesion example-surface tension allows spiders to walk on water ___________________-attraction between molecules of different substances-example-water creating meniscus as attaches to sides of graduated cylinder capillary action and how it is used in nature __________________ Draws water out of roots and up into stems and leaves adhesion adhesion HEAT CAPACITY---because of H-bonds ,takes a lot of heat to get water molecules moving faster, creating high heat capacity….helping organisms maintain body temp’s B. Solutions and Suspensions Water is often in a ________________________,where 2 or more elements or compounds are PHYSICALLY combined mixture Figure 2-9 NaCI Solution Section 2-2 ClCl- Na+ Na+ Water Go to Section: Water Figure 2-9 NaCI Solution Section 2-2 ClCl- Na+ Na+ Water Go to Section: Water 2 types of solutions __________________mixture where components evenly distributed Ions are surrounded by water molecules and evenly distributed _____________-substance dissolved ______________-substance that does dissolving ____________________-mixtures of water and non dissolved materials—blood cells in a suspension of water in vessels solvent solute Solutions suspension Acids,Bases and pH- pH Water molecule can react to form ions.Draw reaction as shown @ bottom of p.42: _________________indicates concentration of H ions in solution Each step represents a power of 10example-pH of 5 has 10 x as many H+ ions as same qty of ph 6 ______________-higher concentrations of H+ ions and pH <7 _______________-alkaline-lower H+ concentration and pH>7 ________________weak acids or bases that react w/ strong ones to prevent sharp pH changes acids bases buffers Buffers are dissolved in life’s fluids ,playing an important role in maintaining homeostasis in organisms pH Scale Section 2-2 Increasingly Basic Oven cleaner Increasingly Acidic Neutral Go to Section: Bleach Ammonia solution Soap Sea water Human blood Pure water Milk Normal rainfall Acid rain Tomato juice Lemon juice Stomach acid Interest Grabber Life’s Backbone Section 2-3 Most of the compounds that make up living things contain carbon. In fact, carbon makes up the basic structure, or “backbone,” of these compounds. Each atom of carbon has four electrons in its outer energy level, which makes it possible for each carbon atom to form four bonds with other atoms. As a result, carbon atoms can form long chains. A huge number of different carbon compounds exist. Each compound has a different structure. For example, carbon chains can be straight or branching. Also, other kinds of atoms can be attached to the carbon chain. Go to Section: Interest Grabber continued Section 2-3 1. On a sheet of paper, make a list of at least ten things that contain carbon. 2. Working with a partner, review your list. If you think some things on your list contain only carbon, write “only carbon” next to them. 3. If you know other elements that are in any items on your list, write those elements next to them. Go to Section: Concept Map Section 2-3 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 Go to Section: Carbon, hydrogen, oxygen which contain which contain Carbon,hydrogen, oxygen, nitrogen, phosphorus Carbon, hydrogen,oxygen, nitrogen, III. Carbon Compounds In the 1800’s,chemists thought compounds created by living things –organic compounds-were much different than others In 1838 a German chemist made the organic compound,urea ,from nonorganic ammonium cyanate…Thus principles of chemistry governing nonliving could be applied to living things _________________________is actually the study of almost all C-compounds-many not having anything to do w/ living things. Organic Chemistry A. The Chemistry of Carbon Why is carbon special?---1) It has 4 valence electrons and can make 4 bonds 2)It can bond w/ many other elements. Includes H,O, 3)C can bond to other C’s in single,double or triple bonds 4)C can form chains and rings METHANE ACETYLENE butadiene Isooctane Forms millions of different complex structures. BENZENE RING B. Macromolecules “Giant molecules found in organisms “ Formed by _____________________,in which large compounds are built by joining smaller ones. _______________-small units –join to form ______________-LARGE compounds monomers polymerization polymers The 4 groups of macromolecules are____________________________ Carbohydrates,nucleic acids,lipids and proteins C.Carbohydrates Made up of C,H and O in a ratio 1:2:1. Used by organisms for energy. main source. Used for structure.--by plants and some animals Break down of sugars,like glucose(C6H12O6)provides immediate energyf-or cell activities sucrose Starches are complex carbohydrates-stores extra energy Single sugars are called ______________________,like glucose,galactose and fructose.-CARB MONOMER Sucrose=disaccharide-made of 2 sugars(notice structure in picture) _________________are large molecules formed from monosaccharides polysaccharides Monosaccharides such as glycogen or animal starch—glycogen from the liver helps out when glucose levels run low.This is also stored in muscles for energy. Plants have plant starch and cellulose ,which gives plants their structure----major component of wood and paper. Figure 2-13 A Starch Section 2-3 Starch Glucose Go to Section: D. Lipids Large ,varied group of macromolecules that are generally are ________ in water Includes fats ,oils,waxes Made mostly of C,H and O Groups are ____________________. Can be used to store energy Some are parts of biological membranes or waterproof coverings insoluble Fats,oils,waxes and steroids •Many are formed when glycerol is combined w/ fatty acids 1) If each C atom is joined to another C atom by a single bond it is called _________________.This is because it has the max # of H-atoms.These are________________. solids Saturated fats If there is at least 1 C-C double bond ,it is called ______________________.These are ________________@ room temp.example-olive oil liquids unsaturated If there is more than 1 C-C double bond,it is___________________examples: oils such as corn,sesame,canola and peanut Monomer basically glycerol and fatty acids….see analyzing data,p.48 polyunsaturated E.____________________=macromolecules containing C,H,O,N and P __________________=are polymers assembled from monomers called Nucleic acids nucleotides Nucleotides contain… 1. 5-C sugar 2. phosphate group 3. nitrogenous base Nucleic Acids store and transmit ______________or genetic info… 2 types of nucleic acids 1) _______________-,involved in protein synthesis and has the sugar_________________ . Single strand ribonucleic acid/RNA ribose heredity ___________________________________-contains genetic code and has the sugar ____________________________. Double helix Contains deoxyribose For heredity deoxyribose Deoxyribonucleic acid/DNA _________=macromolecules containing C,H,O and N and composed of amino acids ____________ are compounds w/ an amine group(-NH2) on one end and a carboxyl group(-COOH) on the other end. Look @ Fig 2-16 on p. 47 Proteins Amino acids More than 20 amino acids in nature All amino acids alike in regions where they may be joined by covalent bond.Thus any amino acid can be joined to any amino acid-by bonding an amino group to a carboxyl group The portion of each amino acid that is different is the side chain called a ____group.Some of these R groups are acidic and some are basic…some polar and some nonploar.Some have C rings . The instructions for assembling amino acids into different proteins is stored in____. R DNA Figure 2-16 Amino Acids Section 2-3 Amino group Carboxyl group General structure Go to Section: Alanine Serine Figure 2-17 A Protein Section 2-3 Amino acids Go to Section: Each protein has a specific role….various functions include: control _____________rates. (enzymes). regulate cell processes . forming bones and muscles transporting substances into and out of cells fighting diseases reaction up to 4 levels of organization 1st –sequence of amino acids in a protein chain 2nd –amino acids within a chain can be twisted or folded 3rd –chain itself is folded—If there is more than one chain,each chain has a specific arrangement in space. 4th –Van der Waals forces and H-bonds help maintain a protein’s shape. maintain a protein’s shape. Interest Grabber Section 2-4 Matter and Energy Have you ever sat around a campfire or watched flames flicker in a fireplace? The burning of wood is a chemical reaction—a process that changes one set of chemicals into another set of chemicals. A chemical reaction always involves changes in chemical bonds that join atoms in compounds. The elements or compounds that enter into a chemical reaction are called reactants. The elements or compounds produced by a chemical reaction are called products. As wood burns, molecules of cellulose are broken down and combine with oxygen to form carbon dioxide and water vapor, and energy is released. Go to Section: 1. What are the reactants when wood burns? 2. What are the products when wood burns? 3. What kinds of energy are given off when wood burns? 4. Wood doesn’t burn all by itself. What must you do to start a fire? What does this mean in terms of energy? 5. Once the fire gets started, it keeps burning. Why don’t you need to keep restarting the fire? Go to Section: IV. Chemical Reactions and Enzymes Chemical reactions=_____________________________ Some are fast and some are slow The elements entering into the reaction are _________and that which is produced are the _____________. reactants Process that changes one set of chemicals into another set of chemicals products CO2 + H2OH2CO3 reaction that allows release of CO2 from the bloodstream products reactants Chemical reactions always involve the breaking of bonds in ____________ and the formation of new bonds in _____________. reactants products B. Energy in Reactions Energy is released or absorbed in chemical reactions. 1. Energy ChangesChemical Reactions that release energy are called ______________________ and often occur spontaneously. Example: 2 H2 + O2 2 H2O….energy released as heat/sometimes as light and sound exothermic Chemical reactions that require energy are called_________________ and usually doesn’t occur by itself---NEEDS AN ENERGY SOURCE Example: 2 H2O 2H2 + O2 requires an electrical current endothermic Figure 2-19 Chemical Reactions Section 2-4 Energy-Absorbing Reaction Energy-Releasing Reaction Activation energy Products Activation energy Reactants Reactants Products Go to Section: Organisms must have a source of energy to carry out necessary reactions.Plants get this from products of _________and animals get it from consuming plants or other animals….thus from metabolizing food photosynthesis 2. Activation energy_______________________________________ Energy needed to get a reaction started Effect of Enzymes Section 2-4 Reaction pathway without enzyme Activation energy without enzyme Reactants Reaction pathway with enzyme Activation energy with enzyme Products Go to Section: Enzymes-___________________________ A _________ is a substance that speeds up the rate of a chemical reaction by lowering activation energy. Enzymes speed up reactions that take place in a cell __________________speeds up the release of CO2 from the bloodstream. Enzymes are specific to the reaction they speed up and usually named on the basis of the reaction Proteins that act as biological catalyst catalyst Carbonic anhydrase C. Enzyme Action Reactants must collide w/ sufficient energy to make _____________. product 1. ENZYME-SUBSTRATE COMPLEX-enzymes provide a site where reactants can be brought together to react,thus reducing energy needed for the reaction Reactants of enzyme-catalyzed reactions are called _________________. Enzymes themselves unchanged in a reaction Often end in –ase/sugars in -ose Substrates bind to a site on the enzyme called the _______________.These are complementary shapes..These are bound together by intermolecular forces making an______________These are bound together until the reaction is done. substrates Active site Figure 2-21 Enzyme Action Section 2-4 ADP Enzyme (hexokinase) Substrates Products Glucose-6phosphate Products are released ATP Active site Enzyme-substrate complex Substrates are converted into products Go to Section: Glucose Substrates bind to enzyme REGULATION OF ENZYME ACTIVITY Affected by many variables,such as temperature,pH Cells can regulate enzymes in many ways—often w/ a protein that turns the key enzymes on and off.