Ch. 2 AICE Biological Molecules Notes 2020-2021 PDF

Ch.2: Biological Molecules  Organic Molecules All organic molecules contain carbon What makes carbon so special? Carbon has 4 valence electrons, allowing 4 strong covalent bonds w/ other atoms, including other carbons Carbon atoms can join together to form chains, branched chains, Monomers, Pol...

Ch.2: Biological Molecules  Organic Molecules All organic molecules contain carbon What makes carbon so special? Carbon has 4 valence electrons, allowing 4 strong covalent bonds w/ other atoms, including other carbons Carbon atoms can join together to form chains, branched chains, Monomers, Polymers, and Macromolecules There are 4 main types of organic macromolecules: Carbohydrates Lipids Proteins Nucleic Acids Of these, 3 are polymers – which are large molecules made up of many repeating subunits  Dehydration Synthesis Also known as condensation Monomers to polymers (building) - formation of water  w / pl it “S er ” Hydrolysis Wa t Breaking of bonds between monomers Reaction uses water Polymers to monomers need H2O  Carbohydrates Polymers made of monomers called monosaccharides (single sugars) Monosaccharides contain C, H, & O in 1:2:1 ratio Classified by # of Carbons (trioses, pentoses, hexoses) End in -ose  (CH2O)n General Formula for monosaccharide What would be the formula for a: Triose? Pentose? Hexose?  Pentoses & Shaped in Hexoses ring due to aqueous env. Common pentoses – ribose, deoxyribose Common hexoses – glucose, fructose, galactose  Glucose Most common monosaccharide Carbon atom # 1 joins to oxygen atom on carbon # 5, forms ring, contains 5 carbons & 1 oxygen Carbon # 6 not part of ring Hydroxyl (-OH) group on carbon number 1 may be up or down Up - β-glucose Down - α-glucose Glucose Isomers  Monosaccharide Functions Main source of energy in respiration Are building blocks for larger molecules Ex. Glucose is the monomer for starch, glycogen, cellulose Ex. Ribose is used to make RNA nucleotides and ATP, deoxyribose is used to make DNA nucleotides  Glycosidic Bonds Polar covalent bonds between monosaccharides Allow for the formation of disaccharides and polysaccharides  Polysaccharides May be composed of several thousand monosaccharides Polysaccharides are NOT sugars The most important polysaccharides are starch, glycogen, & cellulose All are made up of glucose monomers  Starch Mixture of ~ 20% amylose & 80% amylopectin Amylose composed of α- glucose molecules, where the 1 carbon of one is bonded to the 4 carbon of another These bonds are called α 1, 4 gylcosidic bonds Creates a spiral shape  Starch cont’d Amylopectin - composed of many 1,4 α- glucose links molecules, as well as α-1,6 links Creates branching  Glycogen Like amylopectin, it is composed of α-glucoses linked w/ 1,4 linkages & 1,6 linkages Glycogen - more branched than amylopectin  Cellulose Polymer of β- glucose molecules, held by 1,4 linkages Glucose in chain is rotated 1800  Cellulose cont’d H+ bonds form between glucose molecules in adjacent chains, forms tightly cross-linked bundles called microfibrils Microfibrils bundle together to form strong cellulose fibers  Structure/ Function Starch & glycogen are both used for energy Starch granules stored in plant cells Glycogen granules stored in animal liver cells Branching structure allows for easy breaking off of glucose molecules for energy  Structure/ Function cont’d The unbranched chains of cellulose allow for the formation of fibers with very high tensile strength Cellulose is one of the main components of cell walls, giving them strength to withstand osmotic pressure Chitin is another polymer made of β- glucose, think of its structure (N)  Lipids Very diverse category Unifying feature - non-polar or insoluble in water Most composed of 1 glycerol molecule bonded to fatty acid chains Fatty acid chains - long hydrocarbon backbone Saturated fatty acids – no double bonds, solid at room temp Unsaturated fatty acids – double bonds, forms kinks in the chain, liquid at room temp  Lipids cont’d Bonds between the glycerol and fatty acids are called ester bonds Triglycerides (fats & oils) are made up of one glycerol molecule with 3 fatty acid chains Serve as energy reserves & to insulate against heat loss  Lipids cont’d Phospholipids - made of 1 glycerol molecule bonded to 1 phosphate group & 2 fatty acid chains Phosphate group “head” - hydrophilic, & the fatty acid “tails” - hydrophobic Forms phospholipid bilayer, makes all cell membranes  Proteins Amino acid monomers Amino acids made of central carbon bonded to amine group, a carboxyl group, and a variable R-group (side- chain) R-group varies for each of the 20 amino acids  Proteins cont’d Peptide bonds form between carboxyl group of 1 amino acid & amine group of another (dehydration synthesis/condensation)  Functions of Proteins Speed up chemical reactions (enzymes) Transport substances across membrane Cell-to-cell communication Fight infections Structural functions Muscle contraction  Proteins cont’d A chain of amino acids linked by peptide bonds = polypeptide 1 protein may consist of > 1 polypeptide chains 4 levels of protein structure  Proteins cont’d Primary Structure Sequence of amino acids linked by peptide bonds Ultimately determines the overall structure of the protein Secondary Structure Caused by hydrogen bonding between the oxygen of the carbonyl group of one amino acid, and the hydrogen on the Secondary Structure cont’d May form corkscrew called α- helix May form β-pleated sheets Other parts of the polypeptide show no regular arrangement Tertiary Structure Complex, 3-D folded shape of polypeptide Caused by interactions between R- groups on amino acids Bonds involved: Hydrogen bonds – weak chemical attractions between polar molecules Disulfide bridges – covalent bonds between cysteine amino acids Ionic bonds – form between ionized amine (NH3+) and carboxylic acid (COO-) groups Hydrophobic interactions – weak interactions between non-polar R groups Quaternary Structure Only certain proteins Association between multiple polypeptide chains, or between a polypeptide & a non-protein component Held together by the same types of bonds seen in tertiary structure  Globular Proteins Somewhat spherical shape Ex. Hemoglobin Oxygen-carrying pigment molecule found in RBCs Made of 2 α-globin polypeptide chains & 2 β-globin chains, each w/ heme group in center Each heme group contains an iron atom, which can bind with one molecule of O2 (when bound to oxygen it is known as oxyhemoglobin)  Fibrous Proteins Proteins that form long strands Ex. Collagen Composed of 3 helix-shaped polypeptide chains (not α-helices) Covalent / H+ bonds hold collagen molecules to one another forming fibrils, and many fibrils bundle to form strong fibers Collagen is flexible, but has a very high tensile strength, so it serves as a structural protein Collagen  Water Because water is polar molecule, it has ability to form hydrogen bonds This ability makes it (arguably) the most important biological molecule Water - most important biological solvent Dissolves ionic & polar substances All biological processes & reactions take place in aqueous solutions High specific heat capacity It takes a lot of energy to change temp. of water Allows cells to resist changes in temp., maintains homeostasis High latent heat of vaporization It takes a lot of heat to cause water to evaporate Allows evaporative cooling – ex. sweat cools us off because large amt. of energy (heat) transferred to sweat to make it evaporate is released  Testing For Biological Macromolecules  Testing for Presence of Sugars Reducing sugars can carry out a process known as reduction, & become oxidized in process Reducing sugars include all monosaccharides & some disaccharides Only common nonreducing sugar is sucrose  Testing for Presence of Sugars Benedict’s test: Benedict’s reagent contains copper(II) sulfate in an alkaline solution and has a distinctive blue color Reducing sugars will reduce soluble blue copper sulfate to insoluble red- brown copper oxide, which is seen as a precipitate Sugar + Cu 2+( benedict’s)  Oxidized sugar + Cu+( red brown  Testing for Presence of Sugars Procedure Add Benedict’s reagent to the solution you are testing and heat it in a water bath (95C) If reducing sugar is present, solution will gradually turn through green, yellow, and orange to red-brown as precipitate is formed As long as excess Benedict’s is used, the intensity of the red color is directly related to the concentration of the reducing sugar Benedict’s Test  Testing for Presence of Sugars Sucrose is a non-reducing sugar, and will NOT yield a pos. Benedict’s test To test for non-reducing sugars, the disaccharide is first broken down into monosaccharides (what chemical process is this?)  Testing for Presence of Sugars Sucrose is a non-reducing sugar, and will NOT yield a pos. Benedict’s test To test for non-reducing sugars, the disaccharide is first broken down into monosaccharides (what chemical process is this?) HYDROLYSIS! This is accomplished with HCl  Testing for Presence of Non-reducing Sugars : Procedure Only conclusive AFTER a negative Benedict’s test Heat sugar solution with HCl Neutralize solution with alkali (ex NaOH) Add Benedict’s reagent and heat in hot water bath If there is a color change and precipitate, there is a non-reducing sugar present in original solution If both a reducing and nonreducing sugar are present, the precipitate obtained will be heavier than the one obtained in the Benedict’s test  Testing for Presence of Starch Starch molecules tend to curl up into long spirals The hole that runs down the middle of the spiral is just the right size for iodine molecules to fit into Testing for Presence of Starch Procedure Iodine solution (Iodine in potassium iodide solution) is orange-brown Add a drop of iodine solution to the substance to be tested A blue-black color is quickly produced if starch is present Iodide Test  Testing for Presence of Lipids Lipids are insoluble in water, but soluble in ethanol (alcohol) This fact is made use of in the emulsion test for lipids Testing for Presence of Lipids Procedure Unknown substance is added to a test tube containing absolute ethanol Stopper test tube and shake vigorously Test tube then poured into test tube of water If lipids are present, a cloudy white suspension is formed  Testing for Presence of Lipids Testing for Presence of Proteins All proteins have peptide bonds which contain nitrogen atoms These form a purple complex with copper (II) ions The reagent used for this test is called biuret reagent  Testing for Presence of Proteins Procedure Add biuret solution to unknown solution to be tested No heating required Purple color indicates that protein is present Develops slowly over several minutes Testing for Presence of Proteins Last year’s results  Pre-Lab: Safety Always wear protective eye goggles and gloves Wear aprons to protect your clothing from staining NEVER direct the open end of a test tube towards another person, including yourself Do not put anything from the lab in your mouth Use caution around heating plates Never reach across test tubes in a hot water bath Pre-Lab Questions 1.) What are 3 types of macromolecules? Give the monomer and polymer names for each type. 2.) What are the reactions that make polymers called? When are these reactions used in the body? 3.) What are the reactions that make monomers from polymers called? When are these reactions used in the body?  Table 1.1 Sample Test Used Observation Conclusion Reducing sugar: Benedict’s test Non-reducing sugar: Hydrolysis with HCl, Control neutralize with NaOH, and Benedict’s test Starch: iodine in potassium iodide solution Reducing sugar test Non-reducing sugar A test Starch test Reducing sugar test Non-reducing sugar B test Starch test Reducing sugar test Non-reducing sugar C test Starch test Reducing sugar test Non-reducing sugar