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Chemistry of Life BIOL-101 Section 800RL Mr. Fusco Chapter 2: The Chemical Context of Life Chapter 3: Water and the Fitness of the Environment Matter Organisms are composed of matter An ______ is a substance that cannot be broken down to other substances by chemical reactions ______ is anything that takes up space or has mass Matter is made up of elements Organized into ______ ______ __ ______ ______ ______ usually first letter or two A ______ is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements Example = Sodium Chloride (NaCl) Fig. 2-3 Compound Example Sodium Chlorine Sodium chloride Essential Elements of Life About 25 of the 94 naturally occurring elements are essential to life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur ______ ______ are those required by an organism in minute quantities (less than 0.01%) What are You Made of? Human composition 1) Oxygen 65% 2) Carbon 18.5% 3) Hydrogen 9.5% 4) Nitrogen 3.3% 5) Calcium 1.5% 6) Phosphorus 1% 7) Potassium 0.4% 8) Sulfur 0.3% 9) Sodium 0.2% 10) Chlorine 0.2% 11) Magnesium 0.1% Trace Elements Micronutrients Minute, “trace”, quantities Vitally Important Ex. cobalt, copper, chromium, fluorine, chlorine, iron, iodine, manganese, selenium and zinc Website defining elements Atoms Each element consists of unique atoms An ______ is the smallest unit of matter that still retains the properties of an element Smallest particle of an element that has the characteristics of that element (elements are built from one kind of atom) Atoms • • Atomic ______ -protons -neutrons Proton number (atomic number) determines the type of element Electrons form a cloud around the nucleus Neutron mass and proton mass are almost identical and are measured in daltons ______ ______ = number of protons ______ ______ = proton # + neutron # Atomic Structure Atomic Structure Particle Symbol Charge Location p+ Mass (amu) 1 Proton Positive (+) Inside Nucleus Neutron n 1 None Inside Nucleus Electron e- .000545 Negative (-) Outside Nucleus Reading the Periodic Table 6 Atomic Number C (# of protons) Atomic Symbol Carbon 12.011 Element Name Atomic mass (# of protons + # of neutrons) Electric Charges The negative charge of the electron is the same magnitude as that of the proton (equal but opposite) An atom is electrically ______ . #protons = #electrons Electron Energy Levels ______ is the capacity to cause change ______ ______ is the energy that matter has because of its location or structure The electrons of an atom differ in their amounts of potential energy An electron’s state of potential energy is called its energy level, or ______ ______ Electron Energy Levels Electrons fill different “shells” -1st shell: up to ______ -2nd shell: up to ______ -3rd shell: up to ______ Shells are filled from inner to outer Atoms will take or give electrons to attain a full outer shell (______ ) Atoms with full shells typically don’t react When drawing an atom like this, it is called a Bohr model. Electron Distribution Electrons help determine the chemical behavior of an atom The periodic table of the elements shows the electron distribution for each element ______ ______ are those in the outermost shell, or ______ ______ Specifically, the chemical behavior of an atom is mostly determined by the valence electrons Elements with a full valence shell are chemically ______(not chemically active) Ions and Isotopes ___________ -(+) or (-) charged particle -What would have to happen for an atom to become an ion? ___________ -atoms of the same element with different numbers of neutrons All atoms of an element have the same number of protons but may differ in number of neutrons Carbon Isotopes: What differs? 12 6 C 13 6 C 14 6 C ___________ 6 neutrons 7 neutrons 8 neutrons Radioactive Isotopes Occurs when nuclei of unstable isotopes break apart Used as ______ in medicine and research Dangers: -Nuclear explosions -Radon (2nd most frequent cause of lung cancer) Some applications of radioactive isotopes in biological research are: Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders Drawing Atoms Using the periodic table, write the following information on your atom on an index card: Symbol Atomic # Atomic mass Element name Sketch your model (Bohr model) Is the outermost electron shell filled Will this element readily react with others? Why or why not? Chemical Bonding Atoms of different elements interact to form ______ These interactions usually result in atoms staying close together, held by attractions called ______ ______ Bonding gives a molecule completely different chemical properties than its parent elements Example: ______ ______, NaCl (table salt) = nontoxic vs. ______ is a metal that is violently reactive with water. If sodium comes into contact with water, the hydrogen gas that is released will actually burst into flames Chemical Bond Types 3 Types of Chemical Bonds -Covalent bond -Ionic bond -Hydrogen bond Covalent Bonds Electron ______ Usually between 2 nonmetals Strongest bond Multiple covalent bonds can form if they need more than one electron to fill their outer shell ______ ______ = sharing of one pair of valence electrons ______ ______ = sharing of two pairs of valence electrons Covalent Bonds The notation used to represent atoms and bonding is called a __________ ________ For example, H–H This can be abbreviated further with a __________ __________ For example, H2 Covalent Bonds Found in most compounds in organisms A ___________ is a group of atoms held together by covalent bonds having no overall charge ________________ is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom, the more strongly it pulls shared electrons toward itself Examples: Sugars, fats, proteins, water What is a diatomic molecule? Polyatomic? Covalent Bond Types ___________ covalent -equally shared electrons ___________ -covalent -One atom has a greater affinity for electrons in a molecule (more electronegative) -Shared electrons will spend more time around that atom -Unequally shared electrons will cause a partial electrical charge (called a _______ ) to form across the molecule Polar vs. Non-Polar Covalent Bonds Non-Polar Covalent Bond Polar Covalent Bond 2 H atoms equally sharing electrons A dipole caused by the polar covalent bond of the water molecule. Weak Bonds Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds, such as ___________ bonds and ___________ bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other Ionic Bonding Electron ___________ Atoms sometimes strip electrons from their bonding partners After the transfer of an electron, both atoms have charges Remember, a charged atom (or molecule) is called an ___________ The oppositely charged ions attract to form an ___________ ___________ An example is the transfer of an electron from sodium to chlorine Ionic Bonding Usually between 2 metals, or a metal and a nonmetal Example: -Na (Sodium) Atomic number = 11 How many electrons in outermost shell? How many electrons to fill outer shell? -Cl (Chlorine) Atomic number 17 How many electrons in outermost shell? How many electrons to fill outer shell? Ionic Bonding: Na and Cl an electron and becomes positively charged (Na+) ___________ ___________ an electron becoming negatively charged (Cl-) Both atoms now become ions ___________ charges on the Na+ and Cl- ions cause them to attract each other and form an ionic bond Na+ + Cl- NaCl ___________ ___________ Ionic Bonding: Na and Cl Ionic Bonding A ___________ is a positively charged ion An ___________ is a negatively charged ion An ionic bond is an attraction between an anion and a cation Compounds formed by ionic bonds are called ionic compounds, or ___________ Salts, such as sodium chloride (table salt), often found in nature as crystals are Hydrogen Bonding Water molecules have polar (charged) ends A ___________ bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom Allows for hydrogen bonding with other water molecules H-bonding holds water molecules together Weak bonds resulting from: -attraction of ___________ ___________ H-atom on 1 water molecule to ___________ ___________ Oatom in another molecule Resulting in water molecules clinging together Water Movie Van der Waals forces Electrons in a molecule are in random motion around the nuclei. The movement of electrons can cause an ___________ distribution of the electron cloud, creating ___________ areas of slightly positive and negative charges When molecules come close together, the attractive forces between these positive and negative regions pull on the molecules and hold them together. The strength of the attraction depends on the size of the molecule, the shape and its ability to attract electrons. Water (Agua) • Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about ___________ water The abundance of water is the main reason the Earth is habitable The water molecule is a ___________ ___________ : The opposite ends have opposite charges ___________ allows water molecules to form hydrogen bonds with each other Properties of Water Four of water’s properties that facilitate an environment for life are: Cohesive/Adhesive behavior High Specific Heat Expansion upon freezing Universal solvent Cohesive Forces ___________ -water molecules are attracted to other water molecules ___________ ___________ = cohesion of water molecules at the surface of a body of water Example:Water strider bug (right) & Basilisk (aka Jesus lizard) Adhesive Forces ___________ -Water is attracted to other materials Example: ______ ______ in a straw -water “climbs” up a straw -water molecules are attracted to the straw molecules -When one water molecule moves closer to the straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw Plants use capillary action to draw water from the ground into themselves High Specific Heat Index Water can absorb a lot of heat before it begins to get hot since -hydrogen bonds ___________ breaking -it takes much energy before bonds break, releases lots before rejoining Example: Moderates temperature on Earth High Specific Heat Index Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat with only a slight change in its own temperature is a measure of the total amount of kinetic energy due to molecular motion ___________ ___________ ___________ ___________ is the energy of motion measures the intensity of heat due to the average kinetic energy of molecules Evaporative Cooling ___________ is transformation of a substance from liquid to gas ___________ ___ ___________ is the heat a liquid must absorb for 1 g to be converted to gas As a liquid evaporates, its remaining surface cools, a process called ___________ ___________ Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water Hottest water molecules leave first, reducing the average temp. of those remaining Examples: -Cools tropical oceans -Keeps coastal areas more moderate Physical States Which is most dense: solid, liquid, gas? Usually solid, but in water, liquid is most dense As a result, when water freezes it floats -hydrogen bonding What if ice did not float? Insulation of Bodies of Water by Floating Ice Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense Water reaches its greatest density at ___________ If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth Universal Solvent Water dissolves more substances than any other liquid. A ___________ is a mix of 2 or more substances A ___________ is a dissolving agent A ___________ is what dissolves Polar substances dissolve in water (like dissolves like) An ___________ solution is one in which water is the solvent Chemical reactions of living things Dissolving animation Hydrophilic & Hydrophobic A ___________ substance is one that has an affinity for water A ___________ substance is one that does not have an affinity for water Oil molecules are hydrophobic because they have relatively nonpolar bonds A ___________ is a stable suspension of fine particles in a liquid Most biochemical reactions occur in water Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution Acids and Bases A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other: The hydrogen atom leaves its electron behind and is transferred as a proton, or ___________ ion (H+) The molecule with the extra proton is now a ___________ ion (H3O+), though it is often represented as H+ The molecule that lost the proton is now a ___________ ion (OH–) Acids and Bases Some water molecules dissociate (come apart) in a solution forming: 1) H+ (hydrogen ions) 2) OH- (hydroxide ion) ___________ release H+ into a solution ___________(alkaline solutions) take in H+ ions and release OH- ions Acids & bases are quantified on a ___________ which is a measure of hydrogen ion concentration in a solution pH Scale Acidic solutions have pH values less than 7 Basic solutions have pH values greater than 7 Water is neutral (pH = 7) Most biological fluids have pH values in the range of 6 to 8 Buffers The internal pH of most living cells must remain close to pH 7 ___________ are substances that minimize changes in concentrations of H+ and OH– in a solution Most buffers consist of an acid-base pair that reversibly combines with H+ The majority of biological processes carried out by cells occur between pH _____________________ . In order to maintain homeostasis it is important to control H+ levels. Have you have ever taken an antacid? This acts as a buffer to help neutralize acids. Your blood contains buffers that keep the pH at 7.4. Threats to Water Quality ___________ ___________ refers to rain, snow, or fog with a pH lower than 5.6 Acid precipitation is caused mainly by the mixing of different pollutants with water in the air and can fall at some distance from the source of pollutants Acid precipitation can damage life in lakes and streams Effects of acid precipitation on soil chemistry are contributing to the decline of some forests Human Activities Human activities such as burning ___________ ___________ threaten water quality ___________ is released by fossil fuel combustion and contributes to: A warming of earth called the “___________ ” effect Acidification of the oceans; this leads to a decrease in the ability of corals to form calcified reefs Questions???