Chapter 2 - Lecture Notes PDF

Fill out as a tool to move toward conceptual understanding Polar Covalent Z Nonpolar 3 Ionic Bond I Hydrogen Bond Covalent 4 Strength...

Fill out as a tool to move toward conceptual understanding Polar Covalent Z Nonpolar 3 Ionic Bond I Hydrogen Bond Covalent 4 Strength Weaker than (strong, weak) Stronger than nonpolar Polar Strongest weak (strong Istill strong) double-bond double-bond triple-bond Single-bond Draw electron interaction H H H between two atoms/ions H C g H H Hold a molecule together OR hold molecules together Atoms participating get partial charge or full charge? Chapter 2 – The Chemical Basis of Life I: Atoms, Molecules, and Water Chapter Outline 1. Atoms 2. Chemical bonds and molecules 3. Chemical reactions 4. Properties of water 5. pH and buffers Remember blue font color marks important ideas and bold marks terms to master 2.1 Atoms 1. Polar v.s nonpolar covalent 2. PH Section 2.1 Learning Outcomes 1. Describe the general structure of atoms 2. Define orbital and electron shell Loading… 3. Relate atomic structure to the periodic table of the elements 4. Quantify atomic mass using units of daltons and moles 5. Explain how a single element may exist in 2 or more forms, called isotopes 6. List the 4 elements that  make up most of the mass 2.1 Atoms Atoms are the smallest functional units of matter that form all chemical substances Atoms cannot be further broken down into other substances by ordinary chemical or physical means An element is a pure substance made up of only 1 kind of atom  2.1 Atoms Atoms Are Composed of Subatomic Particles Three subatomic particles are found within an atom nucleus= where the mass ofctom is. Protons positive charge (+) found in atomic - nucleus. Neutrons electrically neutral 3. Electrons - Loading… found in atomic nucleus negative charge (-) found in orbitals around the nucleus - # e- same as # p+ Atomic # = # of protons Each elements has an: Atomic mess = Atomic Number: #p+ Protons + neutrons Atomic Mass: #p+ + #n (has units grams/mole)  2.1 Atoms Electrons Occupy Orbitals/Shells Around an Atom’s Nucleus Valence electrons are electrons in the outermost shell Valence electrons can participate in the formation of chemical bonds Draw an atom with atomic number: 2 6 12 p+ n0 17 1st: up to 2 e- 18 What is the atomic mass (with 2nd: up to 8 e- units) of an element with 12 protons, 12 electrons, and 15 neutrons? 3rd, 4th, 5th, etc: up to 8 e- 2.1 Atoms Isotopes Vary in Their Number of Neutrons Many elements exist in multiple forms, called isotopes, that differ in the number of neutrons they contain Ex: Carbon isotopes 12C contains 6 protons and 6 neutrons 14C contains 6 protons and 8 neutrons 2.1 Atoms All Organisms Are Largely Composed of Four Elements 2.2 Chemical Bonds and Molecules Section 2.2 Learning Outcomes 1. Compare and contrast the types of chemical bonds and atomic interactions (covalent, ionic, hydrogen, van Der Waals) that lead to the formation of molecules 2. Explain the concept of electronegativity and how it contributes to the formation of polar and nonpolar covalent bonds 3. Describe how a molecule’s shape is important to its ability to 2.2 Chemical Bonds and Molecules A molecule contains 2 or more atoms that are bonded together A compound is a molecule that contains different kinds of atoms CO2 ↑ O2 compound - ↑ molecule C6H12O - 6 Molecular formulas are used to represent molecules Chemical symbols represent the elements and the subscript indicates how many of each atom are present  2.2 Chemical Bonds and Molecules Atoms form chemical bonds to fill vacancies in their valence electron shell Loading… Chemical Bond Types are: 1. Ionic bonds 2. Covalent bonds 3. Hydrogen bonds 2.2 Chemical Bonds and Molecules Bond Type #1: Atoms become ions when they give away or take ONE electron to achieve a complete valence shell away give - i el nueil full e- e- 2 3 p+ 3 p+ n0 n0 e- 2 e- = size not to scale 2.2 Chemical Bonds and Molecules Bond Type #1: Atoms become ions when they give away or take ONE electron to achieve a complete valence shell ⑳ ↓ ② 100 e- e- e- e- e- p+ 9 9 p+ n0 n0 e- e- e- e- e- = size not to scale  weak 2.2 Chemical Bonds and Molecules Ionic = bond Bond Type #1: Ions are free, fully charged molecules when they are in water When water evaporates, the positive and negative ions attract each other in Ionic Bonds, resulting in crystals/solids In absence of water, pos and neg ions attract each other in IONIC BONDS. Ions move freely Ions separate when water is added again. around in water  Couclent = Strong 2.2 Chemical Bonds and Molecules Bond Type #2: Covalent bonds form when atoms share a pair of electrons Covalent bonds are strong chemical bonds 2.2 Chemical Bonds and Molecules Bond Type #2: Covalent bonds form when atoms share a pair of electrons Covalent bonds are strong chemical bonds H H C H = H 2.2 Chemical Bonds and Molecules Bond Type #2: Covalent bonds form when atoms share a pair of electrons Type #2a: Nonpolar covalent bonds Some atoms share electrons equally in nonpolar covalent bonds. How do we know C and H share e- equally? 2.2 Chemical Bonds and Molecules Type #2a: Nonpolar covalent bonds How equally electrons are shared between atoms depends on the difference in electronegativity (EN) between the atoms. EN is the ability of an atom to strip electrons away from another atom. Na H C N Cl O EN scale: Atoms with equal or similar EN share electrons equally in nonpolar covalent bonds. Biol 190 students do not have to know EN values. But know: C-H = nonpolar bond O- C, O-H, C-N, N-H = polar 3 2.2 Chemical Bonds and Molecules Type #2b: Polar covalent bonds How equally electrons are shared between atoms depends on the difference in electronegativity (EN) between the atoms. EN is the ability of an atom to strip electrons away from another atom. Na H C N Cl O Atoms with differing EN share electrons unequally in polar covalent bonds. Oxygen bond to any atom is usually polar covalent bond. Biol 190 students do not have to know EN values. But know: C-H = nonpolar bond O- C, O-H, C-N, N-H = polar  2.2 Chemical Bonds and Molecules Type #2b: Polar covalent bonds The atom with the higher EN will pull its partner’s electron close to its own nucleus. This biases the distribution of electrons closer to the high EN atom, making an uneven electron distribution like shown here: 17 "partial" O H Group work Oxygen is much more EN than Hydrogen. The bond between them is polar covalent. What will the effective charge on Oxygen and Hydrogen atoms be in a molecule of water (H20) ? (answer is either: + or -) Oxygen atomic number = 8 Hydrogen atomic number = 1 Remember that atoms form bonds to fill their valence shell ① ⑩ Ask: what is charge on 1p+ 8p+ 8p+ 1p+ atom before bonding? St S- St Ask: what is charge on 1p+ 8p+ 1p+ atom after bonding? 2.2 Chemical Bonds and Molecules Polar and nonpolar bonds determines a molecule’s solubility in water Nonpolar molecules contain predominantly nonpolar bonds Molecule will repel water (hydrophobic) Examples of nonpolar covalent bonds that are important to remember include C—C C—H Oils, fats, waxes Polar molecules contain many polar bonds Molecule will attract water (hydrophilic) Examples of polar covalent bonds that are important to remember include O—H N—H O—C  Sugars, Proteins, salts, acids, bases 2.2 Chemical Bonds and Molecules Hydrogen Bonds Allow Interactions Between and Within Molecules Bond #3: Hydrogen bonds (interactions, really) form between a hydrogen with partial positive charge and another electronegative atom/molecule Individually, H bonds are weak; they form and break easily Collectively, many H bonds can be strong overall 2.2 Chemical Bonds and Molecules Hydrogen Bonds Allow Interactions Between and Within Molecules Bond #4: Van der Waals attraction Weak interactions between all molecules Arise because of random electron location at any given time +  Indicate how this generic atom will change if it becomes a A) Ion > - Purple ) isotope > nucleus - (neutron will have more or less)  Each image below shows two atoms interacting. 1) Label the type of bond shown in each image. 2) What do the shapes illustrate? 3) What the charges (+ or -) mean? Identify some nonpolar covalent bonds in the molecule. Identify some polar covalent bonds in the molecule. Draw a molecule of water interacting with this molecule.  Group Work Why does table salt (NaCl) dissolve in water? Why does an oil molecule (lipid) NOT dissolve in water? 2.3 Chemical Reactions Section 2.3 Learning Outcomes 1. Define a chemical reaction and give an example of a chemical reaction 2. Relate the concept of a Loading… chemical reaction to the concept of chemical equilibrium 2.3 Chemical Reactions Chemical Reactions Create New Compounds from Elements or Other Compounds A chemical reaction occurs when one or more substances are changed into other substances by making/breaking chemical bonds Properties of chemical reactions: Require a source of energy (heat) for molecules to move and encounter each other In living organisms, they often use an enzyme as a catalyst (to speed up the rate of the reaction) Tend to proceed in a particular direction but will eventually reach equilibrium In living organisms, they usually occur in watery environments 2.3 Chemical Reactions Chemical Reactions Create New Compounds from Elements or Other Compounds Starting materials are called reactants and end materials are called products; in the reaction below, CH4 and O2 are the reactants and CO2 and H2O are the products - ② The bidirectional arrow indicates that the reaction can proceed in both directions Chemical reactions eventually reach a state of equilibrium where the rate of formation of products equals the rate of formation of reactants In biological systems, many reactions do not have a chance to reach equilibrium because products of one reaction may be quickly changed by another reaction  Group work Refer to the following reaction occurring in a solution of water: CO2 + D H2O H2CO3 H+ + HCO3- - -. -0 Given that acids are molecules that release an H+ in water, is H2CO3 an acid or a base? Acid ! 2.4 Properties of Water Section 2.4 Learning Outcomes 1. Define solute and solvent 2. Compare and contrast hydrophilic and hydrophobic substances 3. Explain how solution concentration can be quantified using molarity 4. Describe the 3 states of H2O 5. Make a list of the roles of water that are critical for the survival of living organisms 2.4 Properties of Water Ions and Polar Molecules Readily Dissolve in Water Ions and polar molecules readily dissolve in water; they are called hydrophilic (“water-loving”) Hydrophilic substances can interact with the partial charges on water through electrical attractions 2.4 Properties of Water Ions and Polar Molecules Readily Dissolve in Water Hydrophobic (“water-fearing”) molecules do not dissolve in water Nonpolar molecules (composed predominantly of carbon and hydrogen) do not dissolve in water Nonpolar molecules do not have partial/full charges therefore they are not attracted to water molecules Oil is a familiar example of a nonpolar, hydrophobic substance 2.4 Properties of Water Ions and Polar Molecules Readily Dissolve in Water Hydrophilic = water loving = POLAR= molecules that interact with water Molecules that are hydrophilic have many charged regions to which water molecules are attracted 2.4 Properties of Water Ions and Polar Molecules Readily Dissolve in Water Hydrophobic = water fearing = NONPOLAR = molecules that do not interact with water Molecules that are hydrophobic do not have charged regions that bind water 2.4 Properties of Water Some Molecules Have Both Hydrophilic and Hydrophobic Regions Amphipathic molecules have both polar/ionized and nonpolar regions #1 #2 2.4 Properties of Water Water Performs Many Important Tasks in Living Organisms In addition to acting as a solvent, water serves many other important functions Participates in chemical reactions Provides force or support Removes toxic waste components Evaporative cooling Cohesion and adhesion Surface tension Lubrication 2.5 pH and Buffers Section 2.5 Learning Outcomes 1. Explain how H2O dissociates into hydroxide ions (OH-) and hydrogen ions (H+), and calculate the concentration of hydrogen and hydroxide ions at a given pH 2. Explain the relationship between hydrogen ion concentration and pH value 3. Give examples of how buffers maintain a stable environment in an animal’s body fluids pH is a measure of H+ concentration Determined by the equation: pH = log[H+] H+ ions are also called protons - - -- Hydrogen atom Hydrogen ion (H+) e- 1p+ 1p+ -  More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ LOW H+ H+ HIGH H+ pH H+ H+ H+ pH H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ LOTS H+ H+ H+ H+ LOW pH = H+ H+ H+ H+ H+ H+ of H + H+ H+ H+ H H++ H+ HIGH H+ H+ H+ pH = LESS H+ H+ H+ H+ H+ H+ # of H + H+ H+ H+ H+  More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ LOW H+ H+ HIGH H+ pH H+ H+ H+ pH H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ Importance of pH in biological H+ H+ H H++ H+ systems? H+ H+ SHAPE of a protein determines H+ its FUNCTION! H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ Molecules in Hthe H+ + H+ stomach that work to H+ H+ H+ H+ H+ H+ H+ breakdown large H+ H+ H+ food molecules must H+ H+ H+ H+ operate at pHH+ 2 with H+ H+all these H+ ions in H+ the stomach Hsolution. + H+ H+ H+ H+ H+ H+ H+ H+ H+ H H++ This is the active shape H+ H+ H+ H+ H+ of trypsin, a protein H+ H+ H+ made by yourH+stomach H+ that breaks down food. H+ H+ H+ Tyrpsin binds to H+ ions H+ H+ in stomach fluid to H+ achieve this active shape. H+ More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ Molecules in Hthe H+ + H+ stomach that work to H+ H+ H+ H+ H+ H+ H+ breakdown large H+ H+ H+ food molecules must H+ H+ H+ H+ operate at pHH+ 2 with H+ H+all these H+ ions in H+ the stomach Hsolution. + H+ H+ H+ H+ H+ H+ This is the inactive H+ H+ shape of trypsin. H H++ H+ H+ H+ Without enough H+ H+ H+ H+ Food Hmash + travels ions to bind to, the H+ H+ from stomachH+ protein is denatured H+ (pH2) into intestine and inactive. H+ H+ H+ H+ (pH 8) H+ H+ H+ More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ Molecules in Hthe H+ + H+ stomach that work to H+ H+ H+ H+ H+ H+ H+ breakdown large H+ H+ H+ food molecules must H+ H+ H+ H+ operate at pHH+ 2 with H+ H+all these H+ ions in H+ the stomach Hsolution. H+ H+ Where do the H+ + H+ H+ H+ H+ ions come from? H+ The stomach H+ H+ H H++ H+ continuously H+ H+ H+ H+ produces acids Food Hmash + travels which are molecules H+ H+ from stomachH+(ph2) that release H+ into H+ into intestine (pH the stomach fluid. H+ H+ H+ H+ 8) H+ H+ H+ 2.5 pH and Buffers Hydrogen Ion Concentrations Are Changed by Acids and Bases An acid is a molecule that has a H+ that “falls off” when the molecule is added to a solution acids increase [H+] acids can be called proton donors Ex: A base is a molecule that binds to free H+ when added to a solution bases decrease [H+] Ex: McKinley et al., 2016 McGraw Hill 2.5 pH and Buffers The pH Is a Measure of the H+ Concentration of a Solution Pure water is neutral with a pH of 7 McKinley et al., 2016 McGraw Hill  2.5 pH and Buffers Buffers Minimize Fluctuations in pH A buffer is a molecule (or group of molecules) that prevents pH changes if either excess acid or base is added to a solution buffers accept H+ from excess acid buffers donate H+ to neutralize excess base Your blood and stomach acid is HEAVILY buffered to prevent pH changes. Does alkaline water effect stomach pH? Why or why not? pH=9.5 Assign A) Dissolves in water B) Does not dissolve in water to the terms below: hydrophobic hydrophilic Ions Molecules with Molecules with Fats mostly polar mostly nonpolar covalent bonds covalent bonds oils table sugar table salt acids bases Polar nonpolar  Group work Refer to the following reaction occurring in a solution of water: CO2 + H2O H2CO3 H+ + HCO3- 1. If additional HCO3- was added to this solution, what would happen? The rate of H+ production would increase ) The rate of CO2 production would increase The forward reaction (left to right) would be favored ) The pH of the solution would decrease The solution would become more acidic.I 2 lecture notes : - # of protons = # of electrons + - Atoms are neutral be = # of pi - - # of valence electrons = # of bonds that can be made. Organisms Oxygen, Carbon hydrogen nitrogen - : , , (largely composed of u - noble gases are stable... ONLY bond w/each other.