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Elements & Atoms Created by G.Baker www.thesciencequeen.net Vocabulary I can…. 10/31 – atom 10/31 – I can name 3 elements. 11/3 – element 11/3 – Name the 3 subatomic particles. 11/5 – describe how to calculate neutrons 11/5 – trace elements 11/6 – ions 11/6 – Explain why it is important to know what group and element is located. 11/10 – valance electrons 11/10 - Calculate the charge of an ion of Cl. 11/11 – isotopes 11/13 – explain why compounds form 11/13 – compound 11/14 – activation energy 11/17 – covalent bond 11/11 – Explain why atoms even form ions. 11/14 – Name the parts of a chemical reaction. 11/17 – Which type of bond would be stronger – ionic or covalent? Review Relationship atoms and elements List of elements Element box Subatomic particles – location calculate charge Draw element – bohr’s model 25 elements & symbols 4 main elements in organisms – name 3 trace elements Valence electrons definiions Isotopes – definition and number of neutrons Review • Why do atoms bond? • Name and define the 2 types of bonds • Count atoms in a compound • Define a compound • How can you tell if a bond is ionic or covalent • Draw compounds Why Study Atoms and Elements in BIOLOGY?????? Why Study Atoms in Biology? • Atoms and elements make up our bodies and those of other organisms – They make up the physical environment as well • The ordering of atoms into molecules represents the lowest level of biological organization – Therefore, to understand life, it is important to understand the basic concepts of chemistry Copyright © 2009 Pearson Education, Inc. Name the levels of life from the smallest to the largest!!! Levels of the Organization of Life • Subatomic particle organism • Atom populations • Molecule(compound) community • Organelle ecosystem(biome) • Cell biosphere • Tissue • Organ • Organ system What is this a picture of ? Name 3 facts about this object! ATOMS Atoms: smallest unit of matter that still retains the properties of an element. . Atoms consist of protons, neutrons, and electrons • An atom is the smallest unit of matter that still retains the properties of a element – Atoms are made of over a hundred subatomic particles, but only three are important for biological compounds –Proton—has a single positive electrical charge –Electron—has a single negative electrical charge –Neutron—is electrically neutral Copyright © 2009 Pearson Education, Inc. Protons Protons are located in the nucleus of the atom. They are positively charged. Neutrons Neutrons are located in the nucleus. They have NO charge! Electrons Electrons are located in the shells around the atom. They are negatively charged. Parts of an Atom Protons and neutrons make up the nucleus and has the most mass. Electrons do not weigh as much. SO the atomic mass is only the Protons + the Neutrons Atoms make up substances called elements which are the building blocks of matter. There are 110 elements 1. ELEMENTS ARE PURE SUBSTANCES MADE OF ONLY 1 KIND OF ATOM AND ARE THE BUILDING BLOCKS OF MATTER. 2. ELEMENTS CANNOT BE BROKEN DOWN INTO A SIMPLER SUBSTANCE 3. ELEMENTS HAVE THEIR OWN UNIQUE SET OF PROPERTIES THAT NO OTHER ELEMENT HAS. • ELEMENTS ARE MADE OF ONLY 1 KIND OF ATOM • SOME COMMON ELEMENTS HYDROGEN (H), HELIUM (He), OXYGEN (0), Notice that the first letter is capital and the next letter is lower case. Why Do Some Elements Have Differen Symbols? They are older elements that were name in a different language like Latin. Copper – cuprum Iron – Ferrous Gold - aurum Silver - argentum Elements • Weird written in Latin Rules 1. First letter capital 2. Second letter lower case Living organisms are composed of about 25 chemical elements • Living organisms are composed of matter, which is anything that occupies space and has mass (weight) – Matter is composed of chemical elements –Element—a substance that cannot be broken down to other substances – same atoms –There are 92 elements in nature— only a few exist in a pure state – Life requires 25 essential elements; some are called trace elements Copyright © 2009 Pearson Education, Inc. Essential Elements of Life • About 25 of the 92 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 • Trace elements – elements required by organisms in small amounts. Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Elements in Organisms • 4 elements that make up 96% of human body: Carbon(C), Hydrogen(H), Oxygen(O), Nitrogen(N) 2.2 CONNECTION: Trace elements are common additives to food and water • Some trace elements are required to prevent disease Without iron, your body cannot transport oxygen An iodine deficiency prevents production of thyroid hormones, resulting in goiter Copyright © 2009 Pearson Education, Inc. More about Elements.. • Elements are the building blocks of all matter. • The periodic table is a list of all of the elements that can build matter. It’s a little like the alphabet of chemistry. • The periodic table tells us several things… Created by G.Baker www.thesciencequeen.net Atoms: The Constituents of Matter • Each element contains only one type of atom. • Information on elements is arranged in logical order in a table called the periodic table. • The periodic table arranges elements left to right based on their atomic number, and in columns based on similarities in their properties. Element Info in Each Box Atomic weight Atomic Number Symbol Name Information from the periodic table Atomic Number- Number of Protons in an atom & electrons Silver = 47 protons Atomic Mass - number of protons + neutron To find the Atomic Mass: Round the atomic weight Krypton's mass number is 84 since its atomic weight, 83.80, rounds up to 84. Mass Number = (Number of Protons) + (Number of Neutrons) 84 = 36 + 48 Electrons have special rules…. • You can’t just shove all of the electrons into the first orbit of an electron. • Electrons live in something called shells or energy levels. • Only so many can be in any certain shell. Created by G.Baker www.thesciencequeen.net • Valence electrons are those in the outermost shell, or valence shell • The chemical behavior of an atom is mostly determined by the valence electrons • Elements with a full valence shell are chemically inert or do not react Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Atoms: The Constituents of Matter • The tendency of atoms to be stable when they have eight electrons in their outermost shells is called the rule of eight, or the octet rule. They want their outer shell to be FULL!!!! • This makes them HAPPY!! • Hydrogen and phosphorus are exceptions to the octet rule. Atoms: The Constituents of Matter • The outermost shell of an atom determines how it reacts with other atoms. • Generally, if eight electrons are in the outer shell, the atom is stable and does not tend to react. • Atoms which do not have eight electrons in the outermost shell will share, gain, or lose electrons to arrive at a stable state. Bohr Diagrams DRAW AN ATOM 1) Draw a nucleus with the element symbol inside. Place Protons and neutrons in the nucleus. 2) The electrons will go in the orbits around the nucleus. Fill order of C shells, 2,8,8,18. 3) Place an X over the atom. This splits the atom into quarters. Since electrons are negative and repel each other place electrons into different quarters. Clockwise! 4) Place all electrons until gone! Fig. 2-9 Hydrogen 1H Atomic mass First shell 2 He 4.00 Atomic number Helium 2He Element symbol Electrondistribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Sodium Magnesium Aluminum 12Mg 11Na 13Al Third shell Hydrogen Helium First shell Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Silicon Phosphorus Sulfur Chlorine Argon Second shell Sodium Third shell Magnesium Aluminum PARTS OF PERIODIC TABLE • Number of electrons in the outermost. Determines how the element will bond. GROUPS or family: Columns Number of valence electrons. Group 1 – one valence electron Group 2 – 2 valence electrons Periods - ROWS Rows of elements are called periods. The period number is the number of energy level in that element. Number of electron shells. The number of elements in a period increases as you move down the periodic table because there are more sublevels per level as the energy level of the atom increases. IONS An ion is an atom or molecule with an electrical charge resulting from gain or loss of electrons When an electron is lost, a positive charge results; when one is gained, a negative charge results Two ions with opposite charges attract each other Ions Function • There are nine types of most essential ions of our body which plays a role in supporting and sustaining health and life. • Out of nine, five are positively charged ions and four are negatively charged ions. Ion (Electrolytes) Function • The positively charged ions are called cations ; these are Na+ , K+ , Ca++ , Mg++, and H+ . • The negatively charged ions are called anions ; these are Cl- , HCO3, PO43- , and OH- . Electrolytes Functions • The Sodium (Na+), Chloride (Cl-), Potassium (K+) and Bicarbonate (HCO3-) are called principle electrolytes and are present in the blood and various body fluids. • Potassium (K+) is essential for heart function. • Our kidneys play a vital role in maintaining the electrolyte balance. They filter out excess!! Over work them!!! • The osmosis regulates the movement of water in cells. Theconcentration of electrolytes or ions to a moves water from higher concentration of electrolytes or ions to areas or lower concentration. Isotopes Atoms with the same number of protons, but different numbers of neutrons. Atoms of the same element (same atomic number) with different mass numbers Isotopes of chlorine Atoms consist of protons, neutrons, and electrons • Although all atoms of an element have the same atomic number(protons), some differ in mass number. • Atoms with different numbers of neutrons are isotopes –One isotope of carbon has 8 neutrons instead of 6 (written 14C) –Unlike 12C, 14C is an unstable (radioactive) isotope that gives off energy –Many occur naturally but some are man made Copyright © 2009 Pearson Education, Inc. Learning Check AT 2 Naturally occurring carbon consists of three isotopes, 12C, 13C, and 14C. State the number of protons, neutrons, and electrons in each of these carbon atoms. 12C 13C 14C 6 6 6 #P _______ _______ _______ #N _______ _______ _______ ISOTOPIC NOTATION isotopes are atoms with the same number of protons but different number of neutrons A Z X A = mass number (the total number of protons + neutrons) Z = atomic number (the total number of protons) X = element symbol Figure 2.4 Isotopes Have Different Numbers of Neutrons Atoms: The Constituents of Matter • Some isotopes are radioisotopes, which emit energy as alpha, beta, and gamma radiation from their nuclei. • Radioactive decay transforms the original atom into another atom, usually of another element. Radioactive isotopes can help or harm us • Living cells cannot distinguish between isotopes of the same element – Therefore, when radioactive compounds are used in metabolic processes, they act as tracers – Radioactivity can be detected by instruments • With instruments, the fate of radioactive tracers can be monitored in living organisms Copyright © 2009 Pearson Education, Inc. Radioactive isotopes can help or harm us • Biologists use radioactive tracers in research – Radioactive 14C was used to show the route of 14CO2 in formation of sugar during plant photosynthesis Copyright © 2009 Pearson Education, Inc. Healthy brain Alzheimer’s patient Compounds and Chemical Reactions Created by G.Baker www.thesciencequeen.net Common Compounds for Life • CO2 • H2O • C6H12O6 • NaCl 2.3 Elements can combine to form compounds • Compound—a substance consisting of two or more different elements combined though a chemical reaction! There are many compounds that consist of only two elements – Table salt (sodium chloride or NaCl) is an example – Sodium is a metal, and chloride is a poisonous gas – However, when chemically combined, an edible compound emerges Copyright © 2009 Pearson Education, Inc. How Compounds Form • FOR A COMPOUND TO FORM, A CHEMICAL CHANGE MUST TAKE PLACE (A REACTION) • THE ELEMENTS THAT COMBINE MAKE A NEW SUBSTANCE WITH NEW PHYSICAL PROPERTIES • COMPOUNDS CANNOT BE BROKEN DOWN PHYSICALLY. REQUIRES A CHEMICAL CHANGE • MORE COMMON THAN ELEMENTS Why Do Elements Bond to Form Compounds? Elements bond to fill their outer shell and become stable!!! THEY WANT TO BE HAPPY + Sodium Chlorine Sodium Chloride Sodium Chloride The elements lose their properties in a compound! Chemical Changes Through Chemical Reactions A chemical reaction – Process in which the physical and chemical properties of the original substance change as new substances with different properties are formed http://www.eepybird.com/dc m1.html Gummi Bear Exploding!!!! • Show video of gummi bear and zinc and H gas!!!! Equation for gummi bear 2KClO3 -- 2KCl + O2 melting C6H12O6 +6O2 ----- 6CO2 + 6H2O The energy released is coming from the bonds in the sugar!! This is where we get our energy!!! Instantly, a vigorous, even violent chemical reaction takes place. The oxygen given off by the heated chlorate rapidly attacks the sugars in the candy, transforming them into carbon dioxide gas and water. The resultant energy is given off as light - a *lot* of light as the case turns out. An ex-Army friend of mine compared it to a magnesium flare. The only other product is harmless potassium chloride salt. K+ ions create the light!!!!! Activation energy is the heat which breaks apart the KClO!! CHEMICAL REACTIONS ! Reactants: Zn + I2 Product: Zn I2 Molecules VS. Compounds • Molecules are not compounds • Molecules are not formed by chemical reaction! Created by G.Baker www.thesciencequeen.net What is a Chemical Equation? • A chemical equation is described as a symbolic representation of a chemical reaction. • The reactants of the reaction are found on the left and the products on the right, separated by an equal sign or directional arrows Fig. 2-UN2 2 H2 O2 Reactants 2 H2O Reaction Products • Photosynthesis is an important chemical reaction • Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H20 → C6H12O6 + 6 O2 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-19 Chemical Formula Definition – Short way to write a compound using symbols. Subscript – Small number that is written below the element. Coefficient – The large number in front of the symbols. Ba(OH)2 – . 1) In this compound there are three different elements (Ba), Oxygen (O) and Hydrogen (H). 2) In this compound the subscript 2 goes with the O and H 3) Since Ba is not in the parentheses and it does not have a subscript there is one Ba. 4. Oxygen is in the parentheses and the two elements in the paraentheses so there parentheses are Oxygen (O) and Hydrogen (H) is 2. Same for Hydrogen. Coefficients • In other words a coefficient is used to display 2 or more of the entire unit it appears in front of. The coefficient used in this example shows that, in the left reactant, there are 4 hydrogen, and in the product, there are 4 hydrogen and 2 oxygen. • The coefficient does not effect the oxygen in the reactant because it is not a compound with hydrogen but is separated by the plus sign. An ion is an atom, or group of atoms, that has a net positive or negative charge. cation – ion with a positive charge If a neutral atom loses one or more electrons it becomes a cation. Na 11 protons 11 electrons Na+ 11 protons 10 electrons anion – ion with a negative charge If a neutral atom gains one or more electrons it becomes an anion. Cl 17 protons 17 electrons Cl- 17 protons 18 electrons 2.5 Formation of Sodium Ion Sodium atom Na 2-8-1 – e Sodium ion Na + 2-8 ( = Ne) 11 p+ 11 p+ 11 e- 10 e+ 2.5 Why do elements bond? • Elements bond to fill their outer shells. This make the element stable. TO BE HAPPY! • Elements will either gain, lose or share electrons to fill their outer shell. 2.6 Electron arrangement determines the chemical properties of an atom • Atoms want to fill their outer electron shells – To accomplish this, the atom can share, donate, or receive electrons – This results in attractions between atoms called chemical bonds Copyright © 2009 Pearson Education, Inc. Types of Chemical Bonds Chemically combining of two or more atoms 1. Covalent Bonds 2. Ionic Bonds These are not all the bonds but all we are going to cover. 2.7 Ionic bonds are attractions between ions of opposite charge • An ion is an atom or molecule with an electrical charge resulting from gain or loss of electrons When an electron is lost, a positive charge results; when one is gained, a negative charge results • Two ions with opposite charges attract each other When the attraction holds the ions together, it is called an ionic bond Animation: Ionic Bonds Copyright © 2009 Pearson Education, Inc. Ionic Bonds Ionic Bond – valence electrons are TRANSFERRED from one ion to another!!! METAL IS BONDED TO NONMETAL!!!! K F Drawing an Ionic Compound 1. Draw the Lewis Dot structure for the atoms. 2. Show the electron(s) transfering from one atom to another. Ionic Bonds: One Big Greedy Thief Dog! Covalent Bonds • One or more pairs of electrons are shared by two atoms Covalent bonds join atoms into molecules through electron sharing • A covalent bond results when atoms share outer-shell electrons – A molecule is formed when atoms are held together by covalent bonds – EX: H2O, Cl2, H2, CO, – Notice some are the same elements and others are not! Animation: Covalent Bonds Copyright © 2009 Pearson Education, Inc. Covalent Bonds – ARE STRONGER!! • Sharing electrons causes the bond to be more stable • Ionic bonds are weaker: Pulled apart in water! • Usually compounds are liquids or gases! Created by G.Baker www.thesciencequeen.net NONPOLAR COVALENT BONDS when electrons are shared equally – SAME ELEMENT H2 or Cl2 2. Covalent bonds- Two atoms share one or more pairs of outer-shell electrons. Oxygen Atom Oxygen Atom Oxygen Molecule (O2) POLAR COVALENT BONDS Electrons are shared but shared unequally. CHARGED H2O Polar Covalent Bonds: Unevenly matched, but willing to share. Covalent Bond • Electronegativity – HOW BAD DO YOU WANT ELECTRONS. The more you want them the more you pull. Unequal electron sharing creates polar molecules • Atoms in a covalently bonded molecule continually compete for shared electrons – The attraction (pull) for shared electrons is called electronegativity – More electronegative atoms pull harder Copyright © 2009 Pearson Education, Inc. - water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen. 2.9 Unequal electron sharing creates polar molecules • Water has atoms with different electronegativities – Oxygen attracts the shared electrons more strongly than hydrogen – So, the shared electrons spend more time near oxygen – The result is a polar covalent bond Copyright © 2009 Pearson Education, Inc. 2.9 Unequal electron sharing creates polar molecules • In H2O the oxygen atom has a slight negative charge and the hydrogens have a slight positive charge – Molecules with this unequal distribution of charges are called polar molecules Copyright © 2009 Pearson Education, Inc. (–) (–) O H (+) H (+) CARBON SPECIAL – because it has 4 valence electrons and can form bonds with four other elements. BUILDING BLOCKS OF LIFE!!!!! MACROMOLECULES OF CARBON!!!!! Created by G.Baker www.thesciencequeen.net 2.10 Hydrogen bonds are weak bonds important in the chemistry of life • Some chemical bonds are weaker than covalent bonds • Hydrogen, as part of a polar covalent bond, will share attractions with other electronegative atoms – Examples are oxygen and nitrogen • Water molecules are electrically attracted to oppositely charged regions on neighboring molecules – Because the positively charged region is always a hydrogen atom, the bond is called a hydrogen bond Animation: Water Structure Copyright © 2009 Pearson Education, Inc. WATER’S LIFE-SUPPORTING PROPERTIES Copyright © 2009 Pearson Education, Inc. Hydrogen bond 2.11 Hydrogen bonds make liquid water cohesive • Hydrogen bonding causes molecules to stick together, a property called cohesion – Cohesion is much stronger for water than other liquids – This is useful in plants that depend upon cohesion to help transport water and nutrients up the plant Copyright © 2009 Pearson Education, Inc. 2.11 Hydrogen bonds make liquid water cohesive • Cohesion is related to surface tension—a measure of how difficult it is to break the surface of a liquid – Hydrogen bonds are responsible for surface tension Animation: Water Transport Copyright © 2009 Pearson Education, Inc. Adhesion Water-conducting cells Direction of water movement Cohesion 150 µm 2.12 Water’s hydrogen bonds moderate temperature • Because of hydrogen bonding, water has a greater ability to resist temperature change than other liquids – Heat is the energy associated with movement of atoms and molecules in matter – Temperature measures the intensity of heat • Heat must be absorbed to break hydrogen bonds; heat is released when hydrogen bonds form Copyright © 2009 Pearson Education, Inc. 2.13 Ice is less dense than liquid water • Water can exist as a gas, liquid, and solid – Water is less dense as a solid, a property due to hydrogen bonding Copyright © 2009 Pearson Education, Inc. 2.13 Ice is less dense than liquid water • When water freezes, each molecule forms a stable hydrogen bond with four neighbors – A three-dimensional crystal results – There is space between the water molecules • Ice is less dense than water, so it floats Copyright © 2009 Pearson Education, Inc. Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form 2.14 Water is the solvent of life • A solution is a liquid consisting of a uniform mixture of two or more substances – The dissolving agent is the solvent – The substance that is dissolved is the solute Copyright © 2009 Pearson Education, Inc. 2.14 Water is the solvent of life • Water is a versatile solvent that is fundamental to life processes – Its versatility results from its polarity – Table salt is an example of a solute that will go into solution in water – Sodium and chloride ions and water are attracted to each other because of their charges Copyright © 2009 Pearson Education, Inc. Ion in solution Salt crystal 2.15 The chemistry of life is sensitive to acidic and basic conditions • A few water molecules can break apart into ions – Some are hydrogen ions (H+) – Some are hydroxide ions (OH–) – Both are extremely reactive – A balance between the two is critical for chemical processes to occur in a living organism Copyright © 2009 Pearson Education, Inc. 2.15 The chemistry of life is sensitive to acidic and basic conditions • Chemicals other than water can contribute H+ to a solution – They are called acids – An example is hydrochloric acid (HCl) – This is the acid in your stomach that aids in digestion • An acidic solution has a higher concentration of H+ than OH– Copyright © 2009 Pearson Education, Inc. 2.15 The chemistry of life is sensitive to acidic and basic conditions • Some chemicals accept hydrogen ions and remove them from solution – These chemicals are called bases – For example, sodium hydroxide (NaOH) provides OH– that combines with H+ to produce H2O (water) – This reduces the H+ concentration Copyright © 2009 Pearson Education, Inc. 2.15 The chemistry of life is sensitive to acidic and basic conditions • A pH scale (pH = potential of hydrogen) is used to describe whether a solution is acidic or basic – pH ranges from 0 (most acidic) to 14 (most basic) – A solution that is neither acidic or basic is neutral (pH = 7) Copyright © 2009 Pearson Education, Inc. pH scale 0 1 Acidic solution Increasingly ACIDIC (Higher concentration of H+) Battery acid 2 Lemon juice, gastric juice 3 Grapefruit juice, soft drink, vinegar, beer 4 Tomato juice 5 Rain water 6 Human urine Saliva NEUTRAL [H+]=OH–] 7 Pure water Human blood, tears 8 Seawater Increasingly BASIC (Lower concentration of H+) Neutral solution 9 10 Milk of magnesia 11 Household ammonia 12 Household bleach 13 Oven cleaner Basic solution 14 Acidic solution Neutral solution Basic solution 2.16 CONNECTION: Acid precipitation and ocean acidification threaten the environment • When we burn fossil fuels (gasoline and heating oil), airpolluting compounds and CO2 are released into the atmosphere – Sulfur and nitrous oxides react with water in the air to form acids – These fall to Earth as acid precipitation, which is rain, snow, or fog with a pH lower than 5.6 – Additional CO2 in the atmosphere contributes to the “greenhouse” effect and alters ocean chemistry Copyright © 2009 Pearson Education, Inc. 2.17 EVOLUTION CONNECTION: The search for extraterrestrial life centers on the search for water • An important question is, has life evolved elsewhere? – Water is necessary for life as we know it • The National Aeronautics and Space Administration (NASA) has evidence that water was once abundant on Mars – Scientists have proposed that reservoirs of water beneath the surface of Mars could harbor microbial life Copyright © 2009 Pearson Education, Inc. August 1999 September 2005 New deposit Atoms: The Constituents of Matter • All atoms of an element have the same number of protons, but not necessarily the same number of neutrons. • Atoms of the same element that have different atomic weights are called isotopes. Figure 2.4 Isotopes Have Different Numbers of Neutrons Chemical Bonds: Linking Atoms Together • A molecule is two or more atoms bonded together. • A chemical bond is an attractive force that links two atoms together. Chemical Bonds: Linking Atoms Together • A covalent bond is formed by sharing of a pair of electrons between two atoms. • In hydrogen molecules (H2), a pair of electrons share a common orbital and spend equal amounts of time around each of the two nuclei. • The nuclei stay some distance from each other due to mutually repelling positive charges. Figure 2.8 Electrons Are Shared in Covalent Bonds Properties of Molecules Chemical Bonds: Linking Atoms Together • Molecules made up of more than one type of atoms are called compounds. • Every compound has a molecular weight that is the sum of all atoms in the molecule. Chemical Bonds: Linking Atoms Together • Covalent bonds are very strong. • Each covalent bond has a predictable length, angle, and direction, which makes it possible to predict the three-dimensional structures of molecules. • A double covalent bond occurs when atoms share two pairs of electrons; in triple covalent bonds atoms share three electron pairs. Figure 2.10 Covalent Bonding With Carbon Properties of Molecules Chemical Bonds: Linking Atoms Together • Electrons are not always shared equally between covalently bonded atoms. • The attractive force that an atom exerts on electrons is called electronegativity. • When a molecule has nuclei with different electronegativities, an electron spends most of its time around the nucleus with the greater electronegativity. Chemical Bonds: Linking Atoms Together • Unequal sharing of electrons causes a partial negative charge around the more electronegative atom, and a partial positive charge around the less electronegative atom, resulting in a polar covalent bond. • Molecules that have polar covalent bonds are called polar molecules. Figure 2.11 The Polar Covalent Bond in the Water Molecule Properties of Molecules Chemical Bonds: Linking Atoms Together • Hydrogen bonds may form within or between atoms with polar covalent bonds. • The d– portion of one molecule has a weak attraction to the d+ portion of another molecule. Each of these attractions is called a hydrogen bond. • Hydrogen bonds do not share electrons. • Although hydrogen bonds are weak, they tend to be additive, and they are of profound biological importance. Figure 2.12 Hydrogen Bonds Can Form between or within Molecules Properties of Molecules Chemical Bonds: Linking Atoms Together • Ionic bonds involve a complete transfer of one or more electrons. • Ions are formed when an atom loses or gains electrons. • Positively charged ions are called cations. • Negatively charged ions are called anions. Figure 2.13 Formation of Sodium and Chloride Ions Properties of Molecules Chemical Bonds: Linking Atoms Together • Ionic bonds are formed by the electrical attraction between ions with opposite charges. • Table salt has chloride and sodium ions, held together by ionic bonds. • When salt is introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds. Figure 2.14 Water Molecules Surround Ions Properties of Molecules Chemical Bonds: Linking Atoms Together • Polar molecules tend to be hydrophilic. Substances that are ionic or polar often dissolve in water due to hydrogen bonds. • Nonpolar molecules are called hydrophobic because they tend to aggregate with other nonpolar molecules. • Nonpolar molecules are also attracted to each other via relatively weak attractions called van der Waals forces. Life and Chemistry: Small Molecules • The Mechanistic View of Life • Atoms: The Constituents of Matter • Chemical Bonds: Linking Atoms Together -------------------------------------------------------• Review: Animation – Electron Shells & Reactivity • Chemical Reactions: Atoms Change Partners • Water: Structure and Properties • Acids, Bases, and the pH Scale • Properties of Molecules Chemical Reactions: Atoms Change Partners • Chemical reactions occur when atoms combine or change partners. • In a chemical reaction, reactants are converted to products. • A chemical reaction can be written as an equation. The equation must balance because matter is neither created nor destroyed. Structure of Propane Source: http://kjd.edu-ctr.pref.kanagawa.jp/edb2/chem/models/3d/Propane.jpg Figure 2.15 Bonding Partners and Energy May Change in a Chemical Reaction Properties of Molecules What’s to Come? Metabolic Pathways Source: http://www.humboldt.edu/~rap1/BiochSupp/PathwayDiagrams/FolMetPath.gif Chemical Reactions: Atoms Change Partners • Changes in energy usually accompany chemical reactions. For example, heat and light are released in the propane reaction. • In living cells, it is unusual to have reactions that release light (exceptions: e.g., firefly) • However, heat is a common product in cellular reactions. Why does a corpse have a much lower body temperature than someone who is living? • Also common are changes in potential energy! Potential Energy • Stored energy, such as that in chemical bonds, is called potential energy and is available for future use. For example, the potential energy in glucose can be used to make ATP. • We can measure the potential energy of molecules and express it in units of heat called calories. • A calorie is the amount of heat required to raise the temperature of one gram of pure water from 14.5°C to 15.5°C. Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 2) Properties of Molecules Water: Structure and Properties Due to its shape, polarity, and ability to form hydrogen bonds, water has some unusual properties. • Ice floats in liquid water; normally the solid form of a substance is more dense than the liquid form. • Water has a high specific heat. • Water has a high heat of vaporization. Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 1) Properties of Molecules Water: Specific Heat • A great deal of heat energy is required to change the temperature of liquid water because the hydrogen bonds must be broken. • Specific heat is the number of calories needed to raise one gram of a substance 1oC. The specific heat of liquid water is 1. • Liquid water has a higher specific heat than most other small molecules in liquid form. Water: Structure and Properties • The heat of vaporization is the amount of heat needed to change a substance from its liquid state to its gaseous state. • A lot of heat is required to change water to a gaseous state because the hydrogen bonds of the liquid water must be broken. • Evaporation has a cooling effect by absorbing calories. (Role of sweating and panting.) • Condensing has the opposite effect, releasing heat. Cohesion and Surface Tension • Source: http://www.npl.co.uk/acoustics/techguides/wetting/images/insect.jpg Water: Structure and Properties • Water has a cohesive strength because of hydrogen bonds. • The cohesive strength of water molecules allows the transport of water from the roots to the tops of trees. • Water has high surface tension, which means that the surface of liquid water is relatively difficult to puncture. Water as a Solvent • Source: http://www.uccs.edu/~rmelamed/MicroFall2002/Chapter%202/water%20solvent.jpg Water: Structure and Properties • Water is the solvent of life. • Living organisms are over 70 percent water by weight and many reactions take place in this watery environment. • A solution is a substance (the solute) dissolved in a liquid (the solvent). Water: Structure and Properties • The mole concept is fundamental to quantitative analysis, which deals with concentrations or the amount of a substance in a solution. • A mole is the amount of a substance in grams whose weight is equal to its molecular weight. For example, methane (CH4) has a mw = 16.04 • One mole of any given compound contains approximately 6.02 x 1023 molecules of that compound (Avogadro’s number). Water: Structure and Properties • A 1 molar (1 M) solution is one mole of a compound dissolved in water to make one liter. • Example: One mole of NaCl is the atomic weight of Na (23) plus the atomic weight of Cl (35.5), or 58.5, in grams. When 58.5 grams of NaCl are dissolved in water to make one liter, the solution is 1 molar. Acids & Bases Source: http://dbhs.wvusd.k12.ca.us/webdocs/AcidBase/Lab-AcidBaseTitration/BottleHCl&NaOH.JPG Acids, Bases, and the pH Scale • Some substances dissolve in water and release hydrogen ions (H+); these are called acids. Their release is called ionization. • Other substances dissolve in water and release hydroxide ions (OH–); these are called bases. • Acids donate H+; bases accept H+. Acids, Bases, and the pH Scale • Acids release H+ ions in solution. • If the reaction is complete, it is a strong acid, such as HCl. • The carboxyl group (—COOH) is common in biological compounds (e.g., amino acids). It functions as an acid because —COOH —COO– + H+ Acids, Bases, and the pH Scale • Bases accept H+ in solution. • NaOH ionizes completely to Na+ and OH–. The OH– absorbs H+ to form water. It is a strong base. • The amino group (—NH2) is an important part of many biological compounds; it functions as a weak base by accepting H+: —NH2 + H+ —(NH3)+ Acids, Bases, and the pH Scale • pH is the measure of hydrogen ion concentration. • It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter. • The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14. • A pH 7 means the concentration of hydrogen ions is 1 x 10–7 moles per liter of water. Figure 2.18 pH Values of Some Familiar Substances Properties of Molecules Acids, Bases, and the pH Scale • A buffer is a mixture of a weak acid and its corresponding base. • Because buffers can react with both added bases and acids, they make the overall solution resistant to pH change. • Buffers illustrate the law of mass action: Addition of reactants to one side of a reaction drives the reaction in the direction that uses that component. Figure 2.19 Buffers Minimize Changes in pH Properties of Molecules Properties of Molecules • Chemists use the characteristics of composition, structure, reactivity, and solubility to help classify molecules. • Two other properties that influence the behavior of molecules are the presence of recognizable functional groups, and the existence of isomers of molecules. Properties of Molecules • Functional groups give specific properties to molecules. • Functional groups are covalently bonded to organic molecules. • Amino acids are biological molecules that contain both a carboxyl group and an amino group. Figure 2.20 Some Functional Groups Important to Living Systems (Part 1) Properties of Molecules Figure 2.20 Some Functional Groups Important to Living Systems (Part 2) Properties of Molecules Figure 2.20 Some Functional Groups Important to Living Systems (Part 3) Properties of Molecules Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms • These interactions usually result in atoms staying close together, held by attractions called chemical bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Covalent Bonds • A covalent bond is the sharing of a pair of valence electrons by two atoms • In a covalent bond, the shared electrons count as part of each atom’s valence shell Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-11 Hydrogen atoms (2 H) Hydrogen molecule (H2) • A molecule consists of two or more atoms held together by covalent bonds • A single covalent bond, or single bond, is the sharing of one pair of valence electrons • A double covalent bond, or double bond, is the sharing of two pairs of valence electrons Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings • The notation used to represent atoms and bonding is called a structural formula For example, H–H • This can be abbreviated further with a molecular formula For example, H2 Animation: Covalent Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-12 Name and Molecular Formula (a) Hydrogen (H2) (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4) ElectronLewis Dot Spacedistribution Structure and filling Model Diagram Structural Formula Fig. 2-12a Name and Molecular Formula (a) Hydrogen (H2) ElectronLewis Dot distribution Structure and Diagram Structural Formula Spacefilling Model Fig. 2-12b Name and Molecular Formula (b) Oxygen (O2) ElectronLewis Dot distribution Structure and Diagram Structural Formula Spacefilling Model Fig. 2-12c Name and Molecular Formula (c) Water (H2O) Lewis Dot Electrondistribution Structure and Structural Diagram Formula Spacefilling Model Fig. 2-12d Name and Molecular Formula (d) Methane (CH4) ElectronLewis Dot distribution Structure and Diagram Structural Formula Spacefilling Model • Covalent bonds can form between atoms of the same element or atoms of different elements • A compound is a combination of two or more different elements • Bonding capacity is called the atom’s valence Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings • Electronegativity 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 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings • In a nonpolar covalent bond, the atoms share the electron equally • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally • Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-13 d– O d+ H H H2O d+ Ionic Bonds • Atoms sometimes strip electrons from their bonding partners • An example is the transfer of an electron from sodium to chlorine • After the transfer of an electron, both atoms have charges • A charged atom (or molecule) is called an ion Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-14-1 Na Cl Na Sodium atom Cl Chlorine atom Fig. 2-14-2 Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl– Chloride ion (an anion) Sodium chloride (NaCl) • A cation is a positively charged ion • An anion is a negatively charged ion • An ionic bond is an attraction between an anion and a cation Animation: Ionic Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings • Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystals Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-15 Na+ Cl– Weak Chemical Bonds • Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules • Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important • Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Hydrogen Bonds • A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom • In living cells, the electronegative partners are usually oxygen or nitrogen atoms Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-16 d d+ Water (H2O) d+ Hydrogen bond d Ammonia (NH3) d+ d+ d+ Van der Waals Interactions • If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge • Van der Waals interactions are attractions between molecules that are close together as a result of these charges Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings • Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-UN1 Concept 2.4: Chemical reactions make and break chemical bonds • Chemical reactions are the making and breaking of chemical bonds • The starting molecules of a chemical reaction are called reactants • The final molecules of a chemical reaction are called products Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings