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Atoms and Bonds What is “stuff” made of? Atoms and Bonds I. Atoms A. Matter 1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. 2. The smallest unit of an element that retains the properties of that element is an atom. 3. Atoms are composed of protons and neutrons in the nucleus, orbited by electrons: Proton: in nucleus; mass = 1, charge = +1 - Defines Element Neutron: in nucleus; mass = 1, charge = 0 Electron: orbits nucleus; mass ~ 0, charge = -1 Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles Proton: in nucleus; mass = 1, charge = +1 - Defines Element Neutron: in nucleus; mass = 1, charge = 0 Electron: orbits nucleus; mass ~ 0, charge = -1 Orbit at quantum distances (shells) Shells 1, 2, and 3 have 1, 4, and 4 orbits (2 electrons each) Shells hold 2, 8, 8 electrons = distance related to energy Neon (Bohr model) Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles 2. Mass = protons + neutrons 8 O 15.99 Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles 2. Mass = protons + neutrons 3. Charge = (# protons) - (# electrons)... If charge = 0, then you have an ...ION Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Some are stable Some are not... they 'decay' - lose the neutron These 'radioisotopes' emit energy (radiation) Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Some are stable Some are not... they 'decay' - lose the neutron These 'radioisotopes' emit energy (radiation) This process is not affected by environmental conditions and is constant; so if we know the amount of parent and daughter isotope, and we know the decay rate, we can calculate the time it has taken for this much daughter isotope to be produced. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Gamma decay - neutron emits energy as a photon - no change in neutron number, mass, or element. Alpha decay - loss of an alpha particle (2 protons and 2 neutrons) from the nucleus. This changes the mass and element. (Uranium with 92 protons decays to Thorium with 90 protons) Beta decay - a neutron changes to a proton, and an electron is emitted. This changes only the element (determined by the number of protons.), but not the mass. (C14 decays, neutron changes to proton, and N14 is produced) - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - So, For 1/2 of them to change, that would be: 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109) - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - So, For 1/2 of them to change, that would be: 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109) - So, divide 3.0 x 1023 by 1.3 x 109 = 2.3 X 1014 atoms/year. - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - So, For 1/2 of them to change, that would be: 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109) - So, divide 3.0 x 1023 by 1.3 x 109 = 2.3 X 1014 atoms/year. - Divide 2.3 x 1014 by 3.65 x 102 days per year = 0.62 x 1012 /day - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - So, For 1/2 of them to change, that would be: 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109) - So, divide 3.0 x 1023 by 1.3 x 109 = 2.3 X 1014 atoms/year. - Divide 2.3 x 1014 by 3.65 x 102 days per year = 0.62 x 1012 /day - Divide 6.2 x 1011 by 24*60*60 = 8.64 x 104) = - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you may be thinking, "be real"! How can we measure something that is this slow?) - Well, 40 grams of Potassium (K) contains: 6.0 x 1023 atoms - So, For 1/2 of them to change, that would be: 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109) - So, divide 3.0 x 1023 by 1.3 x 109 = 2.3 X 1014 atoms/year. - Divide 2.3 x 1014 by 3.65 x 102 days per year = 0.62 x 1012 /day - Divide 6.2 x 1011 by 24*60*60 = 8.64 x 104) = 0.7 x 107 = 7 x 106 = 7 million atoms changing from Potassium to Argon every second!!! This radiation is detectible and measureable...and when it has been measured over the last 100 years, it is always the same. So, not only is there theoretical justification for expecting a constant decay rate, tests have confirmed this expectation. Atoms and Bonds I. Atoms II. Bonds A. Molecules Atoms and Bonds I. Atoms II. Bonds A. Molecules 1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles. Atoms and Bonds I. Atoms II. Bonds A. Molecules 1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles. 2. Bonds form because atoms attain a more stable energy state if their outermost shell is full. It can do this by loosing, gaining, or sharing electrons. This is often called the 'octet rule' because the 2nd and 3rd shells can contain 8 electrons. Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared C. Ionic Bond - transfer of electron and attraction between ions Cl Na Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared C. Ionic Bond - transfer of electron and attraction between ions D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water 1. Structure Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water 1. Structure 2. Properties 2. Properties - liquid at most Earth temperatures - medium for life 2. Properties - liquid at most Earth temperatures - medium for life - universal solvent - dissolves polar and ionic compounds 2. Properties - liquid at most Earth temperatures - medium for life - universal solvent - dissolves polar and ionic compounds - cohesive/adhesive - bonds to itself and other charged matter 2. Properties - liquid at most Earth temperatures - medium for life - universal solvent - dissolves polar and ionic compounds - cohesive/adhesive - bonds to itself and other charged matter - high specific heat - takes large energy change to change temp/state 2. Properties - liquid at most Earth temperatures - medium for life - universal solvent - dissolves polar and ionic compounds - cohesive/adhesive - bonds to itself and other charged matter - high specific heat - takes large energy change to change temp/state - max, density is a 4C... so ice floats 2. Properties - liquid at most Earth temperatures - medium for life - universal solvent - dissolves polar and ionic compounds - cohesive/adhesive - bonds to itself and other charged matter - high specific heat - takes large energy change to change temp/state - max, density is a 4C... so ice floats - dissociates into ions .... 1 x 10-7 molecules in pure water (pH = 7) Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates 1. Structure - monomer = monosaccharide (simple sugar) Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates 1. Structure - monomer = monosaccharide (simple sugar) CnH2nOn glucose, galactose, fructose are hexose sugars 1. Structure - monomer = monosaccharide (simple sugar) CnH2nOn glucose, galactose, fructose are hexose sugars ribose, ribulose, deoxyribose are pentose sugars 1. Structure - monomer = monosaccharide (simple sugar) CnH2nOn glucose, galactose, fructose are hexose sugars ribose, ribulose, deoxyribose are pentose sugars - monomers are linked together into polymers using dehydration synthesis - a removal of a water molecule (dehydration) and the synthesis of a bond. This requires energy and is catalyzed by enzymes in living systems. 1. Structure - monomer = monosaccharide (simple sugar) CnH2nOn glucose, galactose, fructose are hexose sugars ribose, ribulose, deoxyribose are pentose sugars - monomers are linked together into polymers using dehydration synthesis - a removal of a water molecule (dehydration) and the synthesis of a bond. This requires energy and is catalyzed by enzymes in living systems. - polymer = polysaccaharide disaccharide - 2 - sucrose (glucose and fructose) poly's: starch, glycogen, chitin, cellulose Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates C. Proteins C. Proteins 1. Structure monomer = amino acid C. Proteins 1. Structure monomer = amino acid C. Proteins 1. Structure monomer = amino acid polymer = polypeptide - chain 100-300 amino acids long linked together by dehydration synthesis reactions C. Proteins 1. Structure monomer = amino acid polymer = polypeptide - chain 100-300 amino acids long linked together by dehydration synthesis reactions VARIABLE... 20 "letters" can make a very diverse "language" of words... C. Proteins 1. Structure 2. Functions a. energy storage... but since they probably do other things, these are metabolized last... b. structure - after water, animals are mostly protein collagen, elastin, actin, myosin, etc... c. metabolic - enzymes d. transport - in the cell membrane - hemoglobin and other transport proteins e. immunity: antibodies are proteins Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates C. Proteins D. Lipids D. Lipids 1. Structure monomer = fatty acid D. Lipids 1. Structure monomer = fatty acid Mammal, bird, reptile fats - saturated - solid at room temp Plants, fish - often unsaturated - liquid at room temp. Unsaturated fats can be 'hydrogenated' (peanut butter) D. Lipids 1. Structure transfats associated with atherosclerosis D. Lipids 1. Structure polymer = fat (triglyceride) D. Lipids 1. Structure polymer = fat (triglyceride) phospholipid D. Lipids 1. Structure 2. Function a. energy storage - long term - densely packed bonds b. Cell membranes c. insulation d. homones and cholesterol derivatives Atoms and Bonds I. Atoms II. Bonds III. Biologically Important Molecules A. Water B. Carbohydrates C. Proteins D. Lipids E. Nucleic Acids E. Nucleic Acids 1. DNA and RNA Structure a. Monomer = nucleotide - sugar: Ribose in RNA Deoxyribose in DNA E. Nucleic Acids 1. DNA and RNA Structure a. Monomer = nucleotide - sugar: : Ribose in RNA Deoxyribose in DNA - Phosphate group (PO4) E. Nucleic Acids 1. DNA and RNA Structure a. Monomer = nucleotide - sugar: Ribose in RNA Deoxyribose in DNA - Phosphate group (PO4) - Nitrogenous Base DNA = (A, C, G, T) RNA = (A, C, G, U) E. Nucleic Acids 1. DNA and RNA Structure a. Monomer = nucleotide E. Nucleic Acids 1. DNA and RNA Structure 2. DNA and RNA Function a. Information Storage - these nucleic acids are recipes for proteins... the linear sequence of A, T, C, and G's in these molecules determines the linear sequence of amino acids that will be linked together to form a protein. E. Nucleic Acids 1. DNA and RNA Structure 2. DNA and RNA Function a. Information Storage - these nucleic acids are recipes for proteins... the linear sequence of A, T, C, and G's in these molecules determines the linear sequence of amino acids that will be linked together to form a protein. b. Catalytic Action - some RNA molecules catalyze reactions; they act like proteinaceous enzymes. (Ribozymes) E. Nucleic Acids 1. DNA and RNA Structure 2. DNA and RNA Function a. Information Storage - these nucleic acids are recipes for proteins... the linear sequence of A, T, C, and G's in these molecules determines the linear sequence of amino acids that will be linked together to form a protein. b. Catalytic Action - some RNA molecules catalyze reactions; they act like proteinaceous enzymes. (Ribozymes) c. Some RNA molecules bind to RNA or RNA and regulate the expression of these molecules, turning them off.
