Chapter 2 The Chemical Basis of Life Part 1 3.pptx PDF

A Few Things Before We Start My name is Charles Despres I will cover chapters 2 and 3 on weeks 1-3. I will cover many, but not all figures of the textbook. My questions will only be on the Mid-term exam. My questions will only be taken from the slides I present....

A Few Things Before We Start My name is Charles Despres I will cover chapters 2 and 3 on weeks 1-3. I will cover many, but not all figures of the textbook. My questions will only be on the Mid-term exam. My questions will only be taken from the slides I present. I will have no questions at the final exam. All questions will be multiple choices. © McGraw Hill, LLC  Because learning changes everything. ® Chapter 2 The Chemical Basis of Life I: Atoms, Molecules, and Water Lecture Outline BIOLOGY Sixth Edition Robert J. Brooker, Eric P. Widmaier, Linda E. Graham, Peter D. Stiling © 2023 McGraw Hill, LLC. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior written consent of McGraw Hill, LLC.  Key Concepts Atoms Chemical Bonds and Molecules Properties of Water pH and Buffers © McGraw Hill, LLC 3  Matter Matter is anything that has mass and occupies space All life forms are composed of matter Matter can exist in any of three states: solid, liquid, or gas © McGraw Hill, LLC 4  Atoms The smallest functional units of matter that form all chemical substances Cannot be further broken down into other substances by ordinary means Chemists study atoms and molecules, which are two or more atoms bonded together Each specific type of atom is a chemical element © McGraw Hill, LLC 5  Three subatomic particles Protons positive charge (+) found in atomic nucleus Neutrons neutral found in atomic nucleus Electrons negative charge (−) found in orbitals Protons and electrons are present in equal numbers, giving the atom no net charge The number of neutrons can vary © McGraw Hill, LLC 6  Electrons occupy orbitals Scientists initially visualized an atom as a miniature solar system This is an oversimplified but convenient image Electrons travel within regions surrounding the nucleus (orbitals) in which the probability of finding that electron is high Better model of an atom is a central nucleus surrounded by cloudlike orbitals © McGraw Hill, LLC 7  Orbitals s orbitals are spherical p orbitals are propeller or dumbbell shaped Each orbital can hold only 2 electrons © McGraw Hill, LLC 8  Electron Shells Atoms with more electrons have orbitals within electron shells that are at greater and greater distances from the center of the nucleus 1st shell 1 spherical orbital (1s) - holds one pair of electrons 2nd shell 1 spherical orbital (2s) - holds one pair of electrons 3 dumbbell-shaped orbitals (2p) - three pairs of electrons Can hold four pairs of electrons = 8 electrons © McGraw Hill, LLC 9  Example: Nitrogen atom 7 protons and 7 electrons 2 electrons fill 1st shell 2 in the 1s orbital 5 electrons in 2nd shell 2 fill the 2s orbital 1 in each of the three 2p orbitals Note: the outer 2nd shell is not full Electrons in the outer shell available to combine with other atoms are called valence electrons © McGraw Hill, LLC 10  Figure 2.4 a a) Simplified depiction of a nitrogen atom © McGraw Hill, LLC 11  Lewis Structures Here's an example of NH3​(ammonia), where you can observe the lone pair and the bonded pair: https://brilliant.org/wiki/lewis-structure/ © McGraw Hill, LLC  Lewis Structures Bonded pairs are shown as lines as it keeps things neat. Here's an example of H2O (water): https://brilliant.org/wiki/lewis-structure/ © McGraw Hill, LLC  Figure 2.4 b b) Nitrogen atom showing electrons in orbitals © McGraw Hill, LLC 14  Protons Number of protons is what distinguishes one element from another Atomic number Equals number of protons Also equal to the number of electrons in the atom so that the net charge is zero © McGraw Hill, LLC 15  Periodic table Organized by atomic number Rows correspond to number of electron shells Columns, from left to right, indicate the numbers of electrons in the outer shell (the number of valence electrons) Similar properties of elements within a column occur because they have the same number of electrons in their outer shells, and therefore they have similar chemical bonding properties © McGraw Hill, LLC 16  Figure 2.5 © McGraw Hill, LLC 17  Atomic mass Protons and neutrons are nearly equal in mass, and both are more than 1,800 times the mass of an electron Atomic mass scale indicates an atom’s mass relative to the mass of other atoms Most common form of carbon has six protons and six neutrons, is assigned an atomic mass of exactly 12 Hydrogen atom (atomic mass of 1) has 1/12 the mass of a carbon atom Magnesium atom (atomic mass of 24) has twice the mass of a carbon atom © McGraw Hill, LLC 18  Atomic mass in relation to mass of an electron Table 2.1 Characteristics of Major Subatomic Particles Particle Location Charge Mass relative to electron Proton An illustration shows a brightly colored sphere Nucleus +1 1,836 with positive charge. Neutron An uncolored sphere with no charge. Nucleus 0 1,839 Electron Tiny shaded sphere with negative Around the nucleus −1 1 charge. © McGraw Hill, LLC 19  Mass versus weight Weight is derived from the gravitational pull on a given mass A man weighs 154 pounds on Earth On the moon he weighs about 25 pounds On a neutron star’s surface he would weigh 21 trillion pounds His mass is the same in all locations © McGraw Hill, LLC 20  Units Dalton Unit of measurement for atomic mass Also known as atomic mass unit (amu) One Dalton (Da) equals 1/12 the mass of a carbon atom Carbon has an atomic mass of 12 Daltons Mole 1 mole of any element contains the same number of atoms  6.022 1023 Avogadro’s number © McGraw Hill, LLC 21  Isotopes Multiple forms of an element that differ in the number of neutrons 12 C contains 6 protons and 6 neutrons C contains 6 protons and 8 neutrons 14 Atomic masses are averages of the masses of different isotopes of an element Radioisotopes are unstable, emit radiation as they decay Radioisotopes used in medicine for cancer treatment, imaging (PET scan) © McGraw Hill, LLC 22  Figure 2.6 Steven Needell/Science Source © McGraw Hill, LLC 23  Hydrogen, oxygen, carbon, & nitrogen Make up about 95% of the atoms in living organisms Hydrogen and oxygen occur primarily in water Nitrogen is found in proteins Carbon is the building block of all living matter Mineral elements - less than 1% Trace elements - less than 0.01% Yet they are essential for normal growth and function © McGraw Hill, LLC 24  Table 2.2 Table 2.2 Chemical Elements Essential for Life in Many Organisms* Most abundant in living organisms (approximately 95% of total mass) Element Symbol % Human body mass % All atoms in human body Oxygen O 65 25.5 Carbon C 18 9.5 Hydrogen H 9 63.0 Nitrogen N 3 1.4 Mineral elements (less than 1% of total mass) Calcium Ca Potassium K Chlorine Cl Sodium Na Magnesium Mg Sulfur S Phosphorus P Trace elements (less than 0.01% of total mass) Boron B Manganese Mn Chromium Cr Molybdenum Mo Cobalt Co Selenium Se Copper Cu Silicon Si Fluorine F Tin Sn Iodine I Vanadium V Iron Fe Zinc Zn *Although these are the most common elements in living organisms, many other trace and mineral elements have reported functions. For example, aluminum is believed to be a cofactor for certain chemical reactions in animals, but it is generally toxic to plants. © McGraw Hill, LLC 25  Chemical Bonds and Molecules Molecule Two or more atoms bonded together Molecular formula Contains chemical symbols of the elements in the molecule (C6H12O6) Subscript indicates how many of each atom are present (H2O has two hydrogens, 1 oxygen) Compound Any molecule composed of two or more elements H2O; C6H12O6 Properties of a compound can be drastically different than the properties of the individual elements in the compound © McGraw Hill, LLC 26  Three types of bonds Covalent Bond Electrons are shared to fill valence shells Can be polar covalent or nonpolar covalent Hydrogen Bond Hydrogen atom from one polar molecule is attracted to an electronegative atom from another molecule Ionic Bond Electrons are transferred, forming ions that are attracted to each other © McGraw Hill, LLC 27  Covalent bonds Atoms share a pair of electrons Occurs between atoms with unfilled outer electron shells Covalent bonds are strong chemical bonds, because the shared electrons behave as if they belong to each atom Can share … 1 pair of electrons – single bond, example 2 pairs of electrons – double bond, example 3 pairs of electrons – triple bond, example © McGraw Hill, LLC 28  Figure 2.7 © McGraw Hill, LLC 29  Octet rule Atoms are stable when their outer shell is full For many atoms, the outer shell is filled with 8 electrons (“the octet rule”) An exception is hydrogen, which fills its outer shell with just 2 electrons © McGraw Hill, LLC 30  Figure 2.8 © McGraw Hill, LLC 31  Figure 2.9 © McGraw Hill, LLC 32  Polar covalent bonds Form between atoms of different electronegativity (attraction to electrons) Shared electrons are more likely to be close to the more electronegative atom The unequal distribution of electrons creates a polarity (difference in electric charge) across the molecule Examples include O-H and N-H © McGraw Hill, LLC 33  Nonpolar covalent bonds Between atoms with similar electronegativities (attraction to electrons) Equal sharing of electrons No charge difference across molecule Examples include C-C and C-H © McGraw Hill, LLC 34  Figure 2.10 © McGraw Hill, LLC 35  Hydrogen bonds The hydrogen atom from one polar molecule is attracted to an electronegative atom of another Represented as dashed or dotted lines Individually, these are weak bonds that can form and break easily Collectively, many H bonds can be strong overall Holds DNA strands together Enzymes are molecules that catalyze biologically important chemical reactions Small molecules may bind to enzymes via hydrogen bonds © McGraw Hill, LLC 36  Figure 2.11 © McGraw Hill, LLC 37  van der Waals dispersion forces Another type of weak molecular attraction Arise because electrons are located within orbitals in a random way A fleeting electrical attraction to other nearby molecules may arise Collective strength can be quite strong © McGraw Hill, LLC 38  Ionic bonds An ion is an atom or molecule that has gained or lost one or more electrons Cations – have a net positive charge (+) Anions – have a net negative charge (−) Ionic bond occurs when a cation binds to an anion by electrostatic attraction Example is NaCl, table salt © McGraw Hill, LLC 39  Figure 2.12 b: Charles D. Winters/Science Source © McGraw Hill, LLC 40  Table 2.3 Table 2.3 Ionic Forms of Some Common Elements in Living Organisms Atom Chemical Ion Ion Electrons symbol symbol gained or lost Calcium Ca Calcium ion Ca2+ 2 lost Chlorine Cl Chloride ion Cl 1 gained Hydrogen H Hydrogen ion H 1 lost Magnesium Mg Magnesium ion Mg2+ 2 lost Potassium K Potassium ion 1 lost K+ Sodium Na Sodium ion Na  1 lost © McGraw Hill, LLC 41  Molecules May Change Their Shapes Atoms combine to form a molecule with three dimensional shape The shape is determined by the arrangement and number of bonds between atoms Angles that form between atoms give molecules specific shapes Covalent bonds are not rigid and rotation around single covalent bonds allows molecules to change shape The binding of one molecule to another can cause the molecule to change shape © McGraw Hill, LLC 42  Figure 2.13 © McGraw Hill, LLC 43  Figure 2.14 © McGraw Hill, LLC 44  Free radicals Molecule containing an atom with a single, unpaired electron in its outer shell Highly reactive molecules; can “steal” an electron from other molecules Can form by exposure to radiation and some toxins Examples are O.-2 ,. OH, NO. Can cause cell damage Can kill invading bacteria Benefits of antioxidants – protective compounds that can donate electrons without becoming highly reactive themselves © McGraw Hill, LLC 45  Chemical Reactions When one or more substances are changed into other substances Reactants → products Properties of chemical reactions Require a source of energy In living organisms, they often require an enzyme as catalyst – speeds reaction rate Tend to proceed in a particular direction but will eventually reach equilibrium Occur in liquid (water) © McGraw Hill, LLC 46  Properties of Water 1 Bodies of all organisms largely composed of water Up to 95% of the weight of certain plants comes from water. 60 to 70% of human body weight comes from water Water is an important liquid in the surrounding environments of many organisms Most chemical reactions in nature involve molecules that are dissolved in water, including reactions inside cells © McGraw Hill, LLC 47  Figure 2.15 © McGraw Hill, LLC 48  Properties of Water 2 Solution = solutes in a solvent Solutes are dissolved substances Solvent is the liquid In an aqueous solution, water is the solvent Ions and molecules with polar covalent bonds will dissolve in water These are hydrophilic © McGraw Hill, LLC 49  Figure 2.16 © McGraw Hill, LLC 50  Solutes Hydrophilic – “water-loving” Readily dissolve in water Molecules with ionic and/or polar covalent bonds Hydrophobic – “water-fearing” Do not dissolve in water Nonpolar molecules like hydrocarbons, oils Amphipathic – “both loves” Have both polar/ionized and nonpolar regions May form micelles in water Detergent is an amphipathic molecule © McGraw Hill, LLC 51  Figure 2.17 Polar (hydrophilic) regions at the surface of the micelle Nonpolar (hydrophobic) ends are oriented toward the interior of the micelle (top right): Dr Jeremy Burgess/Science Source © McGraw Hill, LLC 52  Measuring solutions Concentration Amount of a solute dissolved in a unit volume of solution 1 gram of NaCl dissolved in 1 liter of water = 1 gram/Liter Molarity Molecular mass is the sum of all the atomic masses of all the atoms in the molecule Molarity = Number of moles of a solute dissolved in 1 Liter of water 1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass © McGraw Hill, LLC 53  H2O in three states of matter Solid (ice), liquid (water), and gas (water vapor) Changes in state, such as changes between the solid, liquid, and gas states of H2O, involve an input or release of energy Heat of vaporization – energy to boil Heat of fusion – energy to melt Specific heat is the amount of heat energy to raise temperature 1° Celsius Water is extremely stable as a liquid, due to high heats of vaporization and fusion, and high specific heat © McGraw Hill, LLC 54  Figure 2.18 © McGraw Hill, LLC 55  Colligative properties of water Properties that depend strictly on the total number of dissolved solute particles, not on the type of solute Temperature at which a solution freezes or boils is influenced by amounts of dissolved solutes Addition of solutes to water lowers the freezing point below 0° Celsius raises the boiling point above 100° Celsius Antifreeze (ethylene glycol) lowers the freezing point of the water and prevents it from freezing in cold weather © McGraw Hill, LLC 56  Not just a solvent Water has many important functions in living organisms: Participates in chemical reactions (hydrolysis or condensation) Provides force or support Removes toxic waste components Evaporative cooling Cohesion (molecules of the same type attract each other) and adhesion (unlike molecules attract each other) Surface tension – measure of attraction between molecules at the surface of a liquid Lubrication © McGraw Hill, LLC 57  Figure 2.19 b: Aaron Haupt/Science Source; d: Chris McGrath/Getty Images; e: Dana Tezarr/Getty Images; f: Gallo Images-Anthony Bannister/Getty Images; g: Sergei Mironenko/Shutterstock © McGraw Hill, LLC 58  Acids and Bases 1 Pure water ionizes to a very small extent into hydrogen ions (H ) and hydroxide ions (OH ) In pure water  H   OH   10  7 M  10  7 M 10  14 M © McGraw Hill, LLC 59  Acids and Bases 2 Acids are molecules that release hydrogen ions in solution A strong acid releases more H than a weak acid Bases lower the H concentration Some release OH Others bind H © McGraw Hill, LLC 60  The pH scale pH  log  10  Η  Acidic solutions are pH 6 or below pH 7 is neutral Alkaline solutions are pH 8 or above © McGraw Hill, LLC 61  Figure 2.20 © McGraw Hill, LLC 62  Effects of pH The pH of a solution can affect The shapes and functions of molecules The rates of many chemical reactions The ability of two molecules to bind to each other The ability of ions or molecules to dissolve in water © McGraw Hill, LLC 63  Buffers Organisms usually tolerate only small changes in pH Buffers help to maintain a constant pH An acid-base buffer system can shift to remove or release H to adjust for changes in pH CO2  H2O  H2CO3  H  HCO3- (carbonic acid) (bicarbonate) © McGraw Hill, LLC 64  End Chapter 2 © McGraw Hill, LLC