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Campbell Biology 9th Ed. Chapters 2, 3, 4 & 5 1. Describe the structure of an atom. State which atomic feature determines the identity of the element. Compare & contrast atoms vs. ions. 2. Explain covalent bonding. 3. Distinguish between polar and nonpolar molecules. Give examples. Relate the polarity of a molecule to its behavior in various solutions. 4. Identify the characteristic behavior of water molecules and discuss their significance to living organisms (and the suitability of earth to sustain life) 5. Define acid and base. Explain the relationship between the pH scale and the concentration of hydrogen ions. 6. Explain how carbon’s bonding arrangement allows it to form a variety of structures Note: • Number and orientation of Covalent bonds • Single, double and triple bonds • Ring structures 7. Identify the characteristic functional groups of organic molecules. Relate each functional group to the type of organic molecules possessing it. 8. Distinguish between carbohydrates, lipids, proteins, and nucleic acids. 9. Match monomers with corresponding polymers. Explain the chemical processes which form and break apart polymers. 10. Distinguish between polypeptides and proteins. Explain the four structural levels of proteins. 11. Describe the structure and explain the function of nucleic acids. Distinguish between DNA and RNA. Atoms are the smallest particles of elements, but they consist of even smaller “subatomic” particles; Protons Neutrons and Electrons The number of protons determines the element Particle Location Charge Mass Proton Nucleus Positive 1 AMU Neutron Nucleus Neutral 1 AMU Electron In constant motion outside the nucleus, in regions referred to as orbitals and energy level Negative Negligible (Small enough to ignore relative to the mass of the whole atom) Note the significance of charge. Charged particles will exert forces of attraction and repulsion upon each other. Opposite charges attract. Similar charges repel. Protons in the nucleus are positively charged, so they will repel each other The only way to keep the nucleus from exploding is to keep protons separated, which is accomplished by Neutrons https://www.youtube.com/watch?v=SeDaOigLBTU The number of neutrons may vary for atoms of a particular element. This does not change the identity of the element, but it will affect the stability of the nucleus. Some combinations work better than others The different combinations are called Isotopes https://www.youtube.com/watch?v=SeDaOigLBTU The number of electrons may vary. We generally think of the number of electrons as always being equal to the number of protons, but that isn’t always true. When the number of protons is equal to the number of electrons, the particle is neutral and will be called an Atom. When they aren’t equal, the particle is charged and is called an Ion https://www.youtube.com/watch?v=WWc3k2723IM Because electrons repel each other, they tend to spread out in the space surrounding the nucleus. At greater distances from the nucleus there is more space available. This allows for both more movement and a greater number of electrons. Electrons closer to the nucleus are said to be at “lower energy levels”. Electrons further from the nucleus are at “higher energy levels” http://www.middleschoolchemistry.com/multimedia/chapter4/lesson6 Regions in space where pairs of electrons are likely are called Orbitals. Higher energy levels, being larger, contain greater numbers of orbitals The pattern of orbitals filling is very distinct, and described mathematically In the diagram to the left we see the shapes of the different orbital types. These figures are derived from algebraic equations We describe orbitals by type (“s, p, d, and f”) Each higher energy level contains one additional type of orbital Each additional type has space for more electron pairs (following a pattern of the next odd number; 1, 3, 5, 7 . . .) So the first energy level has only 1 orbital (an “s” orbital). That means the first energy level only has room for 1 pair of electrons All the other energy levels also have an “s” orbital, but also 3 “p” orbitals Those 4 orbitals have room for 4 pairs of electrons (an “octet”) Energy Orbital Number of Level Types Orbitals Max number of electrons 1 s 1 2 2 sp 4 8 3 spd 9 16 4 spdf 16 32 Note that each higher energy level has one more type of orbital than the level before it. Each new type also has a greater number of orbitals: s = 1; p = 3, d = 5, f = 7 Note that the periodic table is organized to demonstrate electron configuration Electron configuration can be used to predict the chemical behavior of elements Because electrons are attracted to the nucleus, they tend to be close to it, at lower energy levels Atoms with larger numbers of electrons will need to have some electrons at higher levels as well The highest energy level used is called the Valence level It is the valence electrons that will form chemical bonds In this Mg atom, the first 2 levels are full. There are 2 electrons in the 3rd level. Those 2 electrons are the valence electrons. When the atom reacts, those 2 valence electrons are lost, leaving behind only the electrons in the first 2 levels (which are full to capacity). It is the unpaired electrons that will tend to be involved in chemical reactions. They may be lost, or the space may be filled by gaining or sharing electrons Lewis Structures are electron dot diagrams that show the valence electrons only Note that the diagrams show the electrons in pairs, because orbitals are electron pairs There are spaces for 4 pairs because there is 1 s orbital and 3 p orbitals Examine each element in this chart and predict the number of chemical bonds that will be formed. Also predict whether electrons will be gained, lost or shared. Note that Ne and Ar have all 4 orbitals completed. The valence level is full to capacity so they are chemically stable, no reaction will occur Li and Na each have only 1 valence electron. It will usually be lost, forming a positively charged ion Ionic bonds happen between ions (not atoms) In this example, Na has lost an electron (+ ion) which Cl has gained (- ion) Oppositely charged ions attract each other Look at the Lewis structures shown for these 2 elements. Na had 1 valence electron. When that electron was lost, it left only the full energy levels behind. The Cl atom had 3 of its 4 orbitals completed. Only 1 orbital contained an unpaired electron. Gaining an electron filled that orbital and created a pair. Covalent bonds are formed when an electron pair is attracted by the nuclei of 2 different atoms simultaneously They form when 2 atoms each have an unpaired electron The bond creates a pair, filling an orbital for both atoms Electronegativity is a number value that describes the relative strength of attraction that an atom will have on a valence electron This helps us to predict what will happen when 2 atoms react For example, if 2 atoms of H collide, each of them will attract a valence electron from the other atom with a relative force of 2.1 Since the attraction force is equal for both atoms, the electron pair will be shared equally As a rule, if the difference between the 2 atoms is 1.7 or greater the bond will be Ionic. If the difference is less than 1.7 the bond will be Covalent If an atom of Na collides with an atom of Cl, the electron pair will be attracted by Na with a force of .9, but by Cl with a force of 3.0. Cl wins. It will take the electron, ionize both, and form an ionic bond In this example, both atoms have an unpaired valence electron. When they collide a chemical bond will form H has an electronegativity of 2.1 and C has an electronegativity of 2.5. Neither can exert a force strong enough to ionize the other. The difference is .4, far below the 1.7 needed to ionize, but not zero. The bond will be covalent, but will have a slight polarity in favor of the C atom, represented by the “dipole” shown The H has a partial + charge, the C has a partial - charge Shape matters. Both of the molecules shown have 3 atoms forming 2 covalent bonds Both of the molecules have a “dipole moment”, meaning the bonds have a polarity The bent shape of the first molecule concentrates the negative charge at one end, but the linear shape of the second molecule puts the polarities directly opposite each other Dipole moment is a vector quantity, it has a magnitude and a direction https://www.youtube.com/watch?v=PVL24HAesnc Use the following electonegativities: H = 2.1, O = 3.5, C = 2.5 Determine the bond polarity for each bond Label each atom as d+ or d – Draw the dipole moment for each bond Predict the polarity of the whole molecule based on shape and bond dipoles Water is special for a number of reasons The bond between H and O is extremely polar. It’s right on the fringe between covalent and ionic The oxygen atom has 2 pairs of unbonded electrons, resulting in both a bent shape and a concentration of negative charge on the oxygen atom The hydrogen has only 1 electron, and it is in the bond between the H and O, leaving the H nucleus exposed at the end of the molecule https://www.youtube.com/watch?v=HVT3Y3_gHGg In the diagrams given, recognize the bent shape, unbonded pairs of electrons, and dipole moment Construct several water molecules with your modeling kit and predict how they will behave towards each other Hydrophilic = Water Loving Hydrophobic = Water Hating Substances that are hydrophilic are attracted to water, and usually dissolved by water Hydrophobic substances have no attraction to water and will not dissolve https://www.youtube.com/watch?v=i3jA40arq9Y Water molecules have strong attractions to each other and to other polar substances Water has a high “specific heat”, and resists temperature change Water absorbs significant amounts of heat energy when it evaporates Water expands when it freezes Water is an excellent solvent of polar and ionic solutes Acid/Base chemistry is dependent upon water https://www.youtube.com/watch?v=iOOvX0jmhJ4 Adhesion and Cohesion both refer to things sticking together. Adhesion Water sticks to something other than water Cohesion Water sticks to itself Strong cohesion between water molecules at the surface can create unusual effects. Note how the water beads up on the surface of the penny. The cohesion forces are stronger than the force of gravity, so the water doesn’t fall off and drop to the table. The insect shown should theoretically sink, but the surface tension is strong enough to support its weight. Watch the videos linked below. You’ll see some interesting effects. https://www.youtube.com/watch?v=ntQ7qGilqZE https://www.youtube.com/watch?v=ynk4vJa-VaQ Compared to other substances, water requires a huge amount of energy to change its temperature. That means that water tends to hold a steady temperature. Consider a rain forest and a desert. Both are hot, but one holds its heat and the other varies temperature drastically from day to night It also means that water can store and move energy very well. The oceans are a huge heat sink https://www.youtube.com/watch?v=dQk5yi05PIk Consider Los Angeles and Phoenix. Almost identical in latitude, but LA has a more moderate climate because the ocean stabilizes the temperature How about Ireland. Further north than Saskatoon, but with a moderate climate. The gulf stream carries warm water from the equator to the European coast and brings heat energy to the British Isles Evaporation is an endothermic reaction. It requires the input of a significant amount of heat energy Sweating doesn’t cool you off. It’s the evaporation of the sweat. As it evaporates it draws heat energy from your body MJ’s sweat isn’t really orange https://www.youtube.com/watch?v=vLfWnX0ahtc The shape and polarity of water molecules cause them to form very distinct arrangements when they crystallize. Note the difference between the molecular arrangement of liquid water and ice. In ice the molecules are closer together, but the crystals contain empty spaces in the hollow part of the molecular bend. Water is the only substance that expands when it freezes. That expansion makes ice less dense than liquid water, causing it to float https://www.youtube.com/watch?v=bzTZx1RDV3w The polarity of water creates a distinct + and – end of the molecule. Those charged regions will pull apart crystals of polar and ionic substances, causing them to dissolve. Ionic substances will not only dissolve, the ions will “dissociate” from each other As the salt dissolves, the Na+ dissociates from the Cl-. Note the orientation of the water molecules relative to the ions in the hydration shells https://www.youtube.com/watch?v=0cPFx0wFuVs The covalent bonds between H and O are so polar they are almost ionic. When water molecules collide, especially when the H from one collides with the O from the other, the H will ionize forming H+ and OH- https://www.youtube.com/watch?v=6gjZ88JbJas On the average, every liter of water has 10-7 moles dissociated into H+ and OH- ions The H+ ion is really a free proton H+ ions form Acids OH- ions form Bases In pure water there is constant activity of the molecules. Some dissociate while others form back in to H2O https://www.youtube.com/watch?v=6gjZ88JbJas Remember that H+ ions make acids, so the greater the concentration of H+ ions, the stronger the acid In pure water, the concentration of H+ ions is 10-7 mol/L The p in pH is a mathematical function (-log). If I look at 10-7 and lose the base 10 and the – sign, I end up with pH = 7 https://www.youtube.com/watch?v=LS67vS10O5Y The word Organic comes from the word Organism Organic compounds are mostly compounds that are formed by living organisms Carbohydrates, Lipids, Proteins and DNA are all organic compounds, but there are others All organic compounds are structured around Carbon The diagram to the right shows an apparatus used for a famous experiment to determine whether organic compounds could be produced from simple inorganic substances without living organisms to direct the reaction Watch the video and read the text Campbell Biology p58-59 https://www.youtube.com/watch?v=gWqJfBEzU98 Carbon has 4 valence electrons, all unpaired, which allows it to form 4 covalent bonds all equally spaced around the carbon in 3 dimensions It bonds readily with H, N, O, S, P and with other C It can form single, double and triple bonds, and ring structures It can form long, stable chains when bonded with other C’s https://www.youtube.com/watch?v=QnQe0xW_JY4 Using your molecular modeling kit, construct 2 carbon hydrocarbon molecules with Only single bonds One double bond One triple bond Note: The number of hydrogens The orientation of the bonds Can the C-C bond rotate freely? The simplest organic compounds are saturated hydrocarbons. Only H and C, with only single bonds There is no limit to the number of carbons in the chain The chart to the left shows names, formulas and structures of some simple “alkanes” https://www.youtube.com/watch?v=UloIw7dhnlQ Because Carbon can form covalent bonds with all the other nonmetals, it can easily bond to something other than H at a given position In the Ethanol shown, an oxygen atom has been substituted on one of the carbon atoms in Ethane Any nonmetal atom or group of nonmetal atoms can be substituted an any position on the chain. The substitution may change the shape, polarity, and behavior of the resulting molecule Using your molecular modeling kit, construct A 2 carbon saturated hydrocarbon with a single substitution A 2 carbon unsaturated hydrocarbon with a single substitution A 2 carbon unsaturated hydrocarbon with 2 different substitutions A 3 carbon saturated hydrocarbon with a single substitution A 4 carbon saturated hydrocarbon with no substitutions https://www.youtube.com/watch?v=22PkbCu3vYI Using your molecular modeling kit, construct: A 2 carbon saturated hydrocarbon (“ethane”) The simplest molecule you can construct using only Oxygen and hydrogen Nitrogen and hydrogen Carbon and oxygen Identify the resulting simple molecules Substitute each onto your ethane molecule (one at a time, please) Each of these functional groups is a characteristic structure that is commonly found in organic molecules Each is fundamentally a simple, inorganic molecule substituted onto the hydrocarbon chain Each will change the shape and polarity of the molecule, causing characteristic chemical behaviors https://www.youtube.com/watch?v=OGD3q1eQ1TE Mono = 1, Poly = many Monomers are simple organic molecules Polymers are larger, more complex molecules that are formed by attaching many monomers together in a chain https://www.youtube.com/watch?v=VigpwmH7E3M Monomer Polymer Simple Sugar Starch Amino Acid Protein Nucleotide DNA or RNA Structures within organisms are built from Carbohydrates (sugars and starches), Proteins, Lipids (fats, oils, waxes and cholesterol), and Nucleic Acids (DNA and RNA) https://www.youtube.com/watch?v=VigpwmH7E3M Carbo = Carbon Hydrate = water = H2O Carbohydrate = CH2O Glucose and Fructose are simple sugars (monosaccharides) consisting of 6 carbon chains or rings (CH2O)6 = C6H12O6 Use your modeling kit to make 6 units of CH2O and link them together(C to C) forming a chain Sucrose is a disaccharide formed by attaching the two simple sugars, glucose and fructose, together as shown Starches (polysaccharides) are polymers formed from attaching many simple sugars into a chain. The chains may be straight or branching, depending on the organism that produces them The diagrams above show some examples of plant and animal starches and the variations in arrangement of the polymer. Amylose, Amylopectin, and Cellulose are plant starches. Glycogen is the main energy storage starch in animal cells Lipids are a large category of chemical compounds with a wide variety of structures and functions In general lipids are categorized together because they are largely hydrocarbons, so they tend to be hydrophobic (not water soluble) Types of Biological Lipids and their Functions: Neutral Fats – Fats and Oils, Food fats Cholesterol – A component of cell membranes and steroid hormones Waxes – form waterproof barriers Phospholipids – largest component of cell membranes Neutral fats consist of fatty acids attached to glycerol (shown at the far left) Since glycerol has only 3 carbons it can only attach up to 3 fatty acids The resulting molecule will be a monoglyceride, diglyceride or triglyceride The fatty acids may be saturated or unsaturated (one or more double bonds) Neutral fats are not technically polymers, because the fatty acids are attached to glycerol, not to each other Cholesterol Steroid Testosterone Cholesterol is a complex lipid with a characteristic ring structure as shown on the diagram Cholesterols vary greatly with regard to the number and position of functional groups Different sterols will have different effects and behaviors depending upon their structure Waxes are long hydrocarbon chains with few if any functional groups They tend to be solid at room temperature because of their high molecular weight, but melt easily because of their low polarity They are hydrophobic, so they are good at forming waterproof barriers Phospholipids are the main component of cell membranes Phospholipids are diglycerides with a phosphate group attached at the 3rd position on the glycerol The phosphate “head” is hydrophilic, while the fatty acid “tails” are hydrophobic Amino acids consist of 4 parts A central carbon ( “alpha”) with 3 attachments An amino group A carboxyl group A side chain (which is variable) In the diagram: a is alpha (note that it is basically a small a with a flourish) R is the organic chemistry equivalent of the algebraic x. It represents a variable There are more than 20 amino acids, but proteins are made from these 20 The shapes, sizes and polarities of the side chains vary, which will affect the function of the protein they form Note that we can categorize the 20 amino acids into smaller groups based on similar structure Amino Acid types: Nonpolar Polar uncharged + charged - charged Aromatic (ring) Amino acids can bind together, attaching the amino group of one to the carboxyl group of the next forming a “peptide” bond Polymer chains of many amino acids are called “polypeptides” Polypeptides then fold up into complex functional shapes, forming proteins The first step in producing a protein is to form the polypeptide There are 20 amino acids. Each position in the polypeptide could be any one of the 20 The sequence of the amino acids is the 1st level, or “primary” structure of the protein The sequence of amino acids is controlled by genetics. A gene is instructions for the AA sequence in the polypeptide Remember that each different amino acid has a different side chain, with a different shape, size, and polarity In the end, the shapes and polarities will affect the overall shape of the protein Remember that the bond angles between the atoms are not nice straight lines, they are bent In a polymer, the bends can be either in the same direction (forming a spiral) or in the opposite direction (forming a zig-zag) Secondary structure is the bending or coiling of the polypeptide Secondary Structure: Spiral = alpha (a) helix ZigZag = beta (b) pleated sheet OK, so some of the side chains were polar, some nonpolar, some +, some -, some even contained sulfur Polar side chains will attract other polar side chains Nonpolar side chains will tend to be pushed away from the water in the cytoplasm + charged side chains will form ionic bonds with – charged side chains, holding them together more firmly than those polar/nonpolar interactions Sulfur containing side chains will form covalent “disulfide bridges” which will lock the fold in place permanently Of course these interactions can be affected by their environment Temperature can affect flexibility Moisture content affects polar/nonpolar interaction pH affects charged regions Extreme heat and harsh chemicals can break disulfide bridges Quaternary structure is really a direct follow-up of tertiary structure The same forces that hold parts of a polypeptide folded together can also hold two different polypeptides together. Many proteins consist of several polypeptides folded together to form a larger structure https://www.youtube.co m/watch?v=zm3kovWpNQ https://www.youtube.co m/watch?v=nEHe3Aie9Ek https://www.youtube.co m/watch?v=yZ2aY5lxEGE https://www.youtube.co m/watch?v=cAJQbSLlonI https://www.youtube.co m/watch?v=Pjt1Q2ZZVjA Please watch the videos and read about protein folding and “chaperonins” on page 85 in your textbook Nucleic Acids are either DNA or RNA They are polymers (generally found in the nucleus) which consist of “nucleotide” monomers Nucleic Acids function for genetic control, which will be studied in far more detail in another unit Individual nucleotides may also serve nongenetic functions Nucleotides are monomers, but are complex molecules in and of themselves They have 3 parts: A pentose sugar, which may be ribose or deoxyribose A phosphate group, actually phosphoric acid A nitrogenous base, of which there are 5 types which fit into 2 categories Ribose and Deoxyribose are both pentose (5 carbon) sugars As the name suggests, deoxyribose is simply ribose with a missing oxygen Deoxyribose is found in DNA, whereas Ribose is in RNA Examine the structures, compare and contrast shapes and functional groups to clarify why such similar molecules might behave differently. The nitrogenous bases are each either a purine or a pyrimidine ring structure. Adenine, Guanine, and Cytosine are found in both DNA and RNA. Thymine in DNA only, Uracil in RNA. The diagram to the left shows DNA (how could you tell?) DNA consists of 2 strands of nucleotide polymers Note the orientation of the strands in comparison to each other Note the nitrogen bases. Do you see a pattern? Note that in RNA, Uracil will take the place of Thymine. Go back a few frames and see why this works In the DNA polymer, Adenine always pairs with Thymine (A-T) and Cytosine with Guanine (G-C) Note the significance of both shape (purine vs pyrimidine) and attraction between functional groups There are a lot of videos available on macromolecules, some are linked below: Khan Academy Playlist (macromolecules) https://www.youtube.com/watch?v=-Aj5BTnzv0&list=PLh4gvBbNMoamw99TjjQCyXKqCsd2HV-k0&index=1 MIT Open Courseware https://www.youtube.com/watch?v=1eGsdK1fPLM Amoeba Sisters https://www.youtube.com/watch?v=YO244P1e9QM Crash Course https://www.youtube.com/watch?v=H8WJ2KENlK0 Bozeman Biology https://www.youtube.com/watch?v=QWf2jcznLsY