Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
AP Bio Chapter 2 Weak bonds intermolecular and intramolecular Hydrogen Van Bonds der Waals Hydrogen Bonds When a hydrogen atom bonded to one molecule is attracted to the slightly negative area (often N or O) of another molecule. Very Can weak individual bond. be a “strong” force if there are many H bonds. Hydrogen Bonds Molecular Shape Determined by the positions of the atom’s orbitals. Molecular Shape Crucial in Biology : determines how most molecules of life recognize and respond to one another. Chemical Reactions The making and breaking of chemical bonds. Reactions do not destroy matter, they only rearrange it. Chemical Equations A way to represent what is happening in a chemical reaction. Ex: 2 H2 + O2 2 H2O Parts of the Equation Reactants: - the starting materials. Products: - the ending materials. Note - all atoms of the reactants must be accounted for in the products. 2 H2 + O2 2 H2O Chemical Equilibrium When the conversion of reactants to products is balanced to the reverse reaction. Ex: 3 H2 + N2 2 NH3 Summary We will now put elements together to form molecules and build the next level in the hierarchy. What is the chemical? Dihydrogen Otherwise monoxide known as H2O Chapter 3 Water and the Fitness of the Environment Question? What molecule Is the most common In living Cells? Water - most cells are 70 - 95% water. The Water Planet Properties Of Water Be ready and able to discuss several of the following properties. 1. Liquid Water Is Cohesive Water sticks to water. Why? Because the polarity of water results in hydrogen bonding. 2. Liquid Water is Adhesive Water sticks to other molecules. Why? Hydrogen bonding. Water transport in trees uses Cohesion and Adhesion 3. Water Has A High Surface Tension The surface of water is difficult to stretch or break. Why? Hydrogen bonding. 4. Water Has A High Specific Heat Specific Heat - the amount of heat needed to raise 1 g of the substance 1 degree C. Why? Hydrogen bonding. Celsius Scale Will be used for most of our temperature measurements. O oC - water freezes 100 oC - water boils 37 oC - human body 5. Water Stabilizes Temperature Water can absorb and store a huge amount of heat from the sun. Result - climate moderation Result - organisms are able to survive temperature changes. Water Has A High Heat Of Vaporization Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it to convert to a gaseous state. Evaporative Cooling Result: Water cools organisms from excessive heat buildup. Why? Hydrogen bonding Water Expands When It Freezes The distance between water molecules INCREASES from the liquid to the solid form. Ice floats Why? Hydrogen bonding Result Aquatic life can live under ice. 6. Water Is A Versatile Solvent Water will form a solution with many materials. Why? it is a polar molecule Solution Homogeneous mixture of two or more substances. Solvent The dissolving agent. Solute The substance that is dissolved. Hydrophilic Materials Materials that Hydro - water philic Have dissolve in water. - to like or love ionic or polar regions (polar covalent bonds) on their molecules for H+ bonds. Hydrophobic Materials that repel water. Hydro - water phobic - to fear Have non-polar covalent bonds. Ex - lipids. Without Water Life Would Not Be Possible!! Solution Concentration Usually Molarity based on Molarity. - the number of moles of solute per liter of solution. Moles: The molecular weight of a substance in grams. One Avogadro’s number of molecules. 6.02 X 1023 Sugar Copper Sulfate Sulfur Mercury Oxide Sodium Chloride Copper Molarity Problem How do you make a 10 % molar solution of sucrose? Comment AP Biology students should be able to calculate solutions in Molarity. Dissociation of Water Water can sometimes split into two ions. In pure water the concentration of each ion is 10-7 M . Adding certain solutes disrupts the balance between the two ions. The two ions are very reactive and can drastically affect a cell. Acids A Substance that increases the H+ conc. Of a solution. Example: HCl HCl H+ + Cl- Acid Rain Acid Rain Bases Substances that reduce the H+ conc. 1. by disassociation 2. by removing H+ from solution Example: NaOH NaOH Na+ + OH- Neutrals Materials that are neither acids nor bases. pH 7 pH Scale A logarithmic scale for showing H+ concentration pH = - log [H+] 0 to 14 pH Scale Example: For a neutral solution: [H+] is 10-7 or - log 10-7 or - (-7) or 7 pH scale Acids: pH <7 etc. Bases: pH >7 etc. Each in H+ pH unit is a 10x change [H+] [OH-] = 10-14 Therefore, if you know the concentration of one ion, you can easily calculate the other. Buffers Substances that minimize changes in H+ and OH- in a solution. Cells --prevent damage. Most biological pH around 0 Carbonic acid: + H2 CO3 HCO3 + H Summary Be able to discuss the properties of water. Be able to measure solution concentrations in Molarity. Be able to work pH scale questions. Describe buffers in the human body. Chapter 4 Carbon and the Molecular Diversity of Life Organic Chemistry The study of carbon compounds. Urea Carbon’s versatility Forms 4 covalent bonds. Molecular shape is tetrahedral. Bonds easily to itself. The electron configuration of carbon gives it compatibility to form covalent bonds with many different elements. The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules. Fig. 4.3 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 3. Variation in carbon skeletons contributes to the diversity of organic molecules Carbon chains form the skeletons of most organic molecules. Skeletons vary in length may be straight, branched, or arranged in closed rings. May also include double bonds. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 4.4 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Isomers Compounds with the same molecular formula but have different structures. Result: Different chemical properties. Which of these are isomers? No Yes Yes No Types Of Isomers 1. 2. 3. Structural Geometric Enantiomers Structural Isomers Different in covalent arrangements of their atoms. Butane Isobutane Geometric Isomers Differ in spatial arrangements. Arise from the inflexibility of double bonds. Enantiomers Molecules that are mirror images of each other. Usually involve an asymmetric carbon. Enantiomers: mirror images Left-handed(L)and right-handed(D) versions. Usually one is biologically active, the other inactive. Enantiomers :four different atoms or groups of atoms bonded to a carbon Fig. 4.6c Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Comment Organisms are sensitive to even the most subtle variations in molecular architecture. Example - Thalidomide Cells can distinguish between two isomers. One is an effective drug. The other causes birth defects. emergent One properties/structure enantiomer of the drug thalidomide reduced morning CHAPTER 4 CARBON AND THE MOLECULAR DIVERSITY OF LIFE Section B: Functional Groups 1. Functional groups contribute to the molecular diversity of life 2. The chemical elements of life: a review Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Functional Groups A group of atoms attached to a carbon skeleton. Involved in chem rx. Hydrophyllic The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. These then interact with different targets in the body. Fig. 4.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Importance of Functional Groups Table 4.1 Functional Groups of Organic Compounds 1.Hydroxyl Group: -OH A hydrogen atom bonded to an oxygen atom. -OH Very polar hydrophilic. Forms alcohols. ethanol 2. Carbonyl Group A carbon atom joined to an oxygen atom by a double bond. Ex. - C=O Two types of Carbonyl Group compounds: Aldehydes—C=O at end Ketones C=O in middle Aldehydes A carbonyl group at the end of a carbon skeleton. Ex. - C=O | H Sometimes written as - CHO Ketones A carbonyl group in the middle of a carbon chain. Ex. -C-C-C|| 0 3. Carboxyl Group Group with a carbon double bonded to an oxygen and to a hydroxyl group. Ex. - C=OH | H Written as: -COOH Also called Carboxylic Acids 4. Amino Group-NH2 Nitrogen bonded to two hydrogens. Act as a base. Part of amino acid 5. Sulfhydryl Group Sulfur bonded to a hydrogen. Ex. -SH Forms compounds called thiols. Helps stabilize protein structure. 6. Phosphate Group Phosphorus with four oxygens. Ex. -PO4 Has a net -2 charge Involved with energy transfers. Summary Be able to recognize isomers. Know/identify the 6 functional groups; properties; where found. 2. The chemical elements of life: a review Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. These elements are linked by strong covalent bonds. Carbon with its four covalent bonds is the basic building block in molecular architecture. The great diversity of organic molecules with their special Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 4.7 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Enantiomers Molecules that are mirror images of each other. Usually involve an asymmetric carbon. Comment Organisms are sensitive to even the most subtle variations in molecular architecture. Example - Thalidomide Cells can distinguish between two isomers. One is an effective drug. The other causes birth defects. 1. Functional groups contribute to the molecular diversity of life The components of organic molecules that are most commonly involved in chemical reactions. Functional groups are attachments that replace one or more hydrogen atoms to the carbon skeleton of the hydrocarbon. Each functional groups behaves consistently from one organic molecule to another. The number and arrangement of Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. These then interact with different targets in the body. Fig. 4.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups. All are hydrophilic and increase the solubility of organic compounds in water. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings CHAPTER 4 CARBON AND THE MOLECULAR DIVERSITY OF LIFE Section B: Functional Groups 1. Functional groups contribute to the molecular diversity of life 2. The chemical elements of life: a review Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Functional Groups A group of atoms attached to a carbon skeleton. Have consistent properties. Their number and kind give properties to the molecule. Importance of Functional Groups Table 4.1 Functional Groups of Organic Compounds Hydroxyl Group A hydrogen atom bonded to an oxygen atom. Ex. -OH Very polar. Allow the material to be hydrophilic. Forms alcohols. Carbonyl Group A carbon atom joined to an oxygen atom by a double bond. Ex. - C=O Two types of Carbonyl Group compounds: Aldehydes Ketones Aldehydes A carbonyl group at the end of a carbon skeleton. Ex. - C=O | H Sometimes written as - CHO Ketones A carbonyl group in the middle of a carbon chain. Ex. -C-C-C|| 0 Carboxyl Group Group with a carbon double bonded to an oxygen and to a hydroxyl group. Ex. - C=OH | H Written as: -COOH Also called Carboxylic Acids Carboxylic Acids H+ (acid). Form many weak organic acids. Donate Amino Group Nitrogen bonded to two hydrogens. Ex. – N-H | H Forms compounds called amines. Act as a base. Sulfhydryl Group Sulfur bonded to a hydrogen. Ex. -SH Forms compounds called thiols. Help with protein structure. Phosphate Group Phosphorus with four oxygens. Ex. -PO4 Has a net -2 charge. Sometimes written as “Pi”. Involved with energy transfers. Summary Be able to recognize isomers. Know the seven functional groups and what properties they give to molecules. 2. The chemical elements of life: a review Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. These elements are linked by strong covalent bonds. Carbon with its four covalent bonds is the basic building block in molecular architecture. The great diversity of organic molecules with their special Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Chapter 5 The Structure and Function of Macromolecules CHAPTER 5 THE STRUCTURE AND FUNCTION OF MACROMOLECULES Section A: Polymer principles 1. Most macromolecules are polymers 2. An immense variety of polymers can be built from a small set of monomers Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Introduction Cells join smaller organic molecules together to form larger molecules. Macromolecules The four major classes: carbohydrates, lipids, proteins, and nucleic acids. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Most macromolecules are polymers Consist of many similar or identical building blocks linked by covalent bonds. The repeated units are small molecules called monomer Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Monomer A building block of a polymer. Condensation Synthesis or Dehydration Synthesis The chemical reaction that joins monomers into polymers. Covalent bonds are formed by the removal of a water molecule between the monomers. Building Polymers: Fig. 5.2a Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Disassembling Polymers: via hydrolysis. “to break with water” Hydrolysis reactions dominate the digestive process, guided by specific enzymes. Fig. 5.2b Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Hydrolysis Reverse of condensation synthesis. Hydro- water Lysis - to split Breaks polymers into monomers by adding water. Four Main Types Of Macromolecules Carbohydrates Lipids Protein Nucleic acids Carbohydrates Used for fuel, building materials, and receptors. Made of C,H,O General formula is CH2O C:O ratio is 1:1 Types Of Carbohydrates Monosaccharides Disaccharides Polysaccharides Monosaccharides Mono - single Saccharide - sugar Simple sugars. 3 to 7 carbons. Can be in linear or ring forms. functions Fuel for cells—esp. glucose Build other macromolecules (rearrangement) Fig. 5.4 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Monosaccharides Can be “Aldoses” or “Ketoses” depending on the location of the carbonyl group. Examples Glucose Galactose Ribose (hexoses) Fructose (pentose) - OSE Word ending common for many carbohydrates. Disaccharides Formed in a dehydration reaction Covalent bond called a “glycosidic linkage” Examples Maltose = glucose + glucose Lactose = glucose + galactose Milk sugar Sucrose Table = glucose + fructose sugar Major transport form of sugar in plants Fig. 5.5a Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Polysaccharides Many joined simple sugars. Used for storage or structure. Examples: Starch-storage in plants Cellulose-plant cell wall; structure Glycogen-animals; energy reserve Chitin-Nitrogen containing;structural; arthropod shell; fungi cell wall; Glucose has 2 possible ring structures. Hydroxyl group, attached to the number 1, carbon may be fixed above (beta glucose) or below (alpha glucose) the ring plane. Fig. 5.7a Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings a glucose and b glucose Starch of 1-4 linkages of a glucose. Linkage makes the molecule form a helix. Fuel storage in plants. Made a glucose Cellulose of 1-4 linkages of b glucose. Linkage makes the molecule form a straight line. Made This allows H atoms on one strand to form hydrogen bonds with OH groups on other strands. Groups of polymers form strong strands, microfibrils, that are basic building material for plants (and humans). Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings b glucose Comment Most organisms can digest starch (1- 4 a linkage), but very few can digest cellulose (1- 4 b linkage). Another example of the link between structure and function. Glycogen “Animal starch” Similar to starch, but has more 1-6 linkages or branches. Found in the liver and muscle cells. Starch Glycogen Chitin Structural polysaccharide Exoskeletons of arthropods (including insects, spiders, and crustaceans). Also fungi cell wall. Similar to cellulose, but,contains a nitrogen appendage. Pure chitin is leathery, but the addition of calcium carbonate hardens the chitin. Fig. 5.9 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Lipids--Introduction Not polymers. Hydrophobic molecules. Structures dominated by nonpolar covalent bonds. Made of C,H,O No general formula. C:O ratio is very high in C. Highly diverse in form and function. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 1. Fats Syn. From Glycerol + fatty acid(s) Glycerol: contains hydroxyl (-OH) group Fatty Acid: A long carbon chain (12-18 C) with a -COOH (acid) on one end and a -CH3 at the other. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Triglyceride/triaclyglycero 3 fatty acids +glycerol Fig. 5.10b Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The 3 Fatty Acids in a FAT can be the Same or Different Variations: Length of chain (# of carbons). # of double bonds Locations of double bonds. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Saturated vs. Unsaturated Fats Saturated Fatty acids No double bonds (between carbons). Straight chains Found in animals Solid at room temp. Factor in atherosclerosis. Unsaturated fatty acids One or more double bonds. Structure has a kink at double bond(s). Plants, fish. Liquid at room temp. Commonly called “oil” Fig. 5.11b Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fats with saturated fatty acids are saturated fats. Most animal fats are saturated. Saturated fats are solid at room temperature. A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits. Fats with unsaturated fatty acids are unsaturated fats. Plant and fish fats, known as oils, are liquid are room temperature. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fat- Functions 1. Long-term Energy storage, esp. in animals- (9kcal/g) : twice as much as carb. It’s more compact than starch or glycogen Cushions Insylates Acid Fat REVIEW: Saturated Fats Unsaturated Fats Saturated - no double bonds. Unsaturated - one or more C=C bonds. Can accept more Hydrogens. Double bonds cause “kinks” in the molecule’s shape. Question ? Which has more energy, a kg of fat or a kg of starch? Fat - there are more C-H bonds which provide more energy per mass. Which is which? Properties? 2. Phospholipids Similar to fats, but have only two fatty acids. The third -OH of glycerol is joined to a phosphate containing molecule (has a negative charge). Be able to draw;labelpolar and nonpolar ends The Result Is… Phospholipids have a hydrophylic head tail, but a hydrophobic tail. Self-assemble into micelles or bilayers, an important part of cell membranes. At the surface of a cell phospholipids are arranged as a bilayer. Again, the hydrophilic heads are on the outside in contact with the aqueous solution and the hydrophobic tails from the core. The phospholipid bilayer forms a barrier between the cell and the external environment. They are the major component of membranes. Fig. 5.12b Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 3. Steroids Lipids with four fused rings. Examples: cholesterol Steroid (sex hormones) Functions off Cholesterol in animals Only in animals. Component in animal cell membranes-stability & insulation. Precursor from which all other steroids are synthesized. Many are hormones, including the vertebrate sex hormones. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Misc. Fat Info Hydrogenation Trans fats Proteins-Introduction Proteins are instrumental in about everything that an organism does. Humans have tens of thousands of different proteins, each with their own structure and function. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Functions Of Proteins Structure Storage Enzymes Antibodies Transport Movement Receptors Hormones Movie Proteins Half the weight of a dry cell. Made of C,H,O,N, and sometimes S. Polymer of amino acids Proteins Polypeptide chains of Amino Acids linked by peptide bonds. One or more polypeptides folded and coiled into specific conformations. Amino Acids All have a Carbon with four attachments: -COOH (acid) -NH2 (amine) -H -R (some other side group) R groups 20 different kinds: Nonpolar Polar - - Electrically Charged Determines the physical & chemical properties of the amino acid. Amino Acids Amino Acids Polypeptides Formed by dehydration synthesis between the carboxyl group of one AA and the amino group of the second AA. Produce a backbone of: (NC-C)X Levels Of Protein Structure Organizing the polypeptide into its 3-D functional shape. Primary Secondary Tertiary Quaternary Primary Sequence of amino acids in the polypeptide chain. Secondary H- Bonds between H and O of backbone Two main secondary structures: a helix pleated sheets Tertiary Bonding between the R groups. Examples: hydrophobic interactions ionic bonding Some disulfide bridges (covalent bond ) s-s form When Quaternary comprised of two or more polypeptides. Examples: hemoglobin enzymes ketatin Is Protein Structure Important? Denaturing Of A Protein Loss of structure (and function). Due to : pH shifts high salt concentrations Heat Example: Egg white cooking Denaturation Nucleic Acids: DNA and RNA Polymers of nucleotides Contain phosphorous Nucleotides have three parts: nitrogenous base pentose sugar phosphate DNA Deoxyribonucleic Acid. Makes up genes. Genetic information source for life. Double stranded molecule. Double helix. Sides– covalent bonds Rungs—hydrogen bonds RNA Ribonucleic 3 Acid. kinds Structure and protein synthesis. Genetic information for a few viruses only. Single-stranded molecule. DNA and RNA More will be said about DNA and RNA in future lessons. Summary For each macromolecule, know the following: Sig. elements and monomers Structures Functions Examples given in class