Transcript ppt
Atoms, Bonds, and Molecules What is “stuff” made of? Atoms and Bonds I. Atoms A. Matter 1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. Atoms and Bonds I. Atoms A. Matter 1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. There are 92 naturally occurring elements… 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. 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 WICKED SMALL and are mostly SPACE. The material ‘things’ in atoms are 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 NOT TO SCALE 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 protons/neutrons 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 protons/neutrons These 'radioisotopes' emit energy (radiation) So, K40, with 19 protons and 21 neutrons, decays to Ar40 (18 protons, 22 neutrons) with the conversion of a proton into a neutron. As neutrons weigh slightly less than protons, the mass that is lost in this conversion is lost as energy (E = mc2) 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 protons/neutrons 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 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 “non-polar” covalent bond…electron pair shared evenly by nuclei. “polar” covalent bond…electron pair shared unevenly by nuclei. 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 Biologically Important Molecules Biologically Important Molecules I. Water Biologically Important Molecules I. Water A. Structure - polar covalent bonds Biologically Important Molecules I. Water A. Structure - polar covalent bonds Biologically Important Molecules I. Water A. Structure - polar covalent bonds - partial charges Biologically Important Molecules I. Water A. Structure - polar covalent bonds - partial charges - hydrogen bonds I. Water A. Structure B. Properties - 1. cohesion “water sticks to itself through H-bonds” I. Water B. Properties - 2. adhesion “water sticks to other charged surfaces” I. Water B. Properties - consequences of cohesion/adhesion Capillary action – rotating water water molecules stick to the inner surface of thin tubes, and act as a fulcrum for other water molecules that can spin and contact the surface above them… through cohesion, those in contact with the new surface are themselves a surface for now water molecules to attach. - important in the mvmt of soil water up from the water table to the root zone, and up vascular plants in xylem tissue. I. Water B. Properties - 3. High specific heat ‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories). I. Water B. Properties - 3. High specific heat ‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories). Water has a high specific heat because of the hydrogen bonds, which must be broken before the molecules can move faster (increase temperature). I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution). I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution). So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…) I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution). So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…) So, terrestrial organisms change temperature more slowly than the environment, giving them time to adjust behaviorally (like leaving!) I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state. I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state. - when it does change state, the most energetic molecules evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling. I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state. - when it does change state, the most energetic molecules evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling. - evaporative cooling keeps water bodies cooler than air, and cools living organisms (evapotranspiration, perspiration). I. Water B. Properties - 6. solvent Ionic and polar compounds dissolve in water Salts dissolve in water when their constituent ions separate and bond to water molecules instead of each other. I. Water B. Properties - 7. Water dissociates Although the H+ is always bound to another water molecule (as a hydronium ion), we represent it (H+) and it’s concentration as if it is ‘free’. In pure water, the concentration is 1 x 10-7. I. Water B. Properties - 7. Water dissociates In all aqueous solutions at 25oC, The product of [H+][OH-] = 1 x 10-14 So, if the pH is 6.0, the concentration of OH- ions is 1 x 10-8 I. Water C. Water and Life Why Life on Earth in Water? I. Water C. Water and Life Life on Earth is inconceivable without water. Life requires rapid and continuous chemical reactions facilitated by a dissolution of reactants in a liquid solvent. Water’s solvent properties are ideal. Water is a liquid over a wide temperature range that is very common on Earth. (High specific heat, vaporization). Water is abundant on Earth, covering over 70% of the surface. Water is a thermally stable internal/external environment. No surprize that life probably originated in water, and did not adapt to exploit the desiccating terrestrial environments until the last 10% of Earth history. Biologically Important Molecules I. Water II. Carbohydrates II. Carbohydrates A. Structure 1. monomer = monosaccharide typically 3-6 carbons, and CnH2nOn formula II. Carbohydrates A. Structure 1. monomer = monosaccharide typically 3-6 carbons, and CnH2nOn formula have carbonyl and hydroxyl groups II. Carbohydrates A. Structure 1. monomer = monosaccharide typically 3-6 carbons, and CnH2nOn formula have carbonyl and hydroxyl groups carbonyl is either ketone or aldehyde in aqueous solutions, they form rings II. Carbohydrates A. Structure 1. monomer = monosaccharide 2. polymerization: dehydration synthesis reaction II. Carbohydrates A. Structure 1. monomer = monosaccharide 2. polymerization 3. Polymers = polysaccharides Disaccharides Polysaccharides Polysaccharides Polysaccharides The ‘cross-linkages’ in cellulose are not digestible by starch-digesting enzymes, so animals cannot eat wood unless they have bacterial endosymbionts. Decomposing fungi and bacteria also have these enzymes, and can access the huge amount of energy in cellulose. Polysaccharides H-bonds link cellulose molecules together Polysaccharides glucosamine II. Carbohydrates A. Structure B. Function - energy storage (short and long) - structural (cellulose and chitin) CO2 Glucose, Cellulose, Starch H2O Biologically Important Molecules I. Water II. Carbohydrates III. Lipids III. Lipids - not true polymers or macromolecules; an assortment of hydrophobic, hydrocarbon molecules classes as fats, phospholipids, waxes, or steroids. III. Lipids A. Fats - structure glycerol (alcohol) with three fatty acids (or triglyceride) III. Lipids A. Fats - structure -saturated fats (no double bonds) Straight chains pack tightly; solid at room temperature like butter and lard. Implicated in plaque buildup in blood vessels (atherosclertosis) Animal fats (not fish oils) III. Lipids A. Fats - structure -unsaturated fats (no double bonds) Plant and fish oils Kinked; don’t pack – liquid at room temperature. “Hydrogenation” can make them saturated and solid, but the process also produces trans-fats (trans conformation around double bond) which may contribute MORE to atherosclerosis than saturated fats) III. Lipids A. Fats - structure - functions - long term energy storage (dense) not vital in immobile organisms (mature plants), so it is metabolically easier to store energy as starch. But in seeds and animals (mobile), there is selective value to packing energy efficiently. In animals, fat is stored in adipose cells III. Lipids A. Fats - structure - functions - long term energy storage (dense) - insulation (subcutaneous fat) - cushioning III. Lipids A. Fats B. Phospholipids - structure Glycerol 2 fatty acids phosphate group (and choline) Hydrophilic and hydrophobic regions III. Lipids A. Fats B. Phospholipids - function selective membranes In water, they spontaneously assemble into micelles or bilayered liposomes. III. Lipids A. Fats B. Phospholipids C. Waxes - structure An alcohol and fatty acid Wax Alcohol Fatty Acid Carnuba CH3(CH2)28CH2-OH CH3(CH2)24COOH Beeswax CH3(CH2)28CH2-OH CH3(CH2)14COOH Spermacetic CH3(CH2)14CH2-OH CH3(CH2)14COOH III. Lipids A. Fats B. Phospholipids C. Waxes - structure - function Retard the flow of water (plant waxes) Structural (beeswax) Signals – waxes on the exoskeleton can signal an insect’s sexual receptivity. III. Lipids A. Fats B. Phospholipids C. Waxes D. Steroids - structure typically a four-ring structure with side groups cholesterol and its hormone derivatives Cholesterol Biologically Important Molecules I. II. III. IV. Water Carbohydrates Lipids Proteins IV. Proteins A. structure - monomer: amino acids IV. Proteins A. structure - monomer: amino acids Carboxyl group Amine group IV. Proteins A. structure - monomer: amino acids 20 AA’s found in proteins, with different chemical properties. Of note is cysteine, which can form covalent bonds to other cysteines through a disulfide linkage. IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis The bond that is formed is called a peptide bond IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide May be 1000’s of aa’s long Not necessarily functional (“proteins” are functional polypeptides) Sequence determines the function IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide - protein has 4 levels of structure 1o (primary) = AA sequence IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide - protein has 4 levels of structure 1o (primary) = AA sequence 2o (secondary) = pleated sheet or helix The result of H-bonds between neighboring AA’s… not involving the side chains. Some proteins are functional as helices - collagen IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide - protein has 4 levels of structure 1o (primary) = AA sequence 2o (secondary) = pleated sheet or helix 3o (tertiary) = folded into a glob The three dimensional structure of the protein is stabilized by all types of bonds between the side chains… ionic between charged AA’s, Hydrogen bonds between polar AA’s, van der Waals forces, and even covalent bonds between sulfurs. IV. Proteins A. structure - monomer: amino acids - polymerization: dehydration synthesis - polymer: polypeptide - protein has 4 levels of structure 1o (primary) = AA sequence 2o (secondary) = pleated sheet or helix 3o (tertiary) = folded into a glob 4o (quaternary) = >1 polypeptide Actin filament in muscle is a sequence of globular actin proteins… 50 myofibrils/fiber (cell) http://3dotstudio.com/prenhall/muscle.jpg IV. Proteins A. structure B. functions! - catalysts (enzymes) - structural (actin/collagen/etc.) - transport (hemoglobin, cell membrane) - immunity (antibodies) - cell signaling (surface antigens) IV. Proteins A. structure B. functions! C. designer molecules If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it? IV. Proteins A. structure B. functions! C. designer molecules If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it? Folding is critical to function, and this is difficult to predict because it is often catalyzed by other molecules called chaparones IV. Proteins A. structure B. functions! C. designer molecules If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it? Folding is critical to function, and this is difficult to predict because it is often catalyzed by other molecules called chaparones Perhaps by analyzing large numbers of protein sequences and structures, correlations between “functional motifs” and particular sequences will be resolved.