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A.C.E. BiologySpring 2011CHAPTER III: The Chemistry of Organic Molecules1CARBOHYDRATESCarbohydrate = CARBON + WATER

(CH2O)n = the empirical formula

MONOSACCHARIDES = simple sugars, of which there are several; C6H12O6 is a simple sugar that exists in several isomeric forms (organic molecules with identical molecular formulas but different arrangements of the atoms comprising the molecules)2GLUCOSE a simple sugar in the form of a six-sided ring (a hexose); holds a place of special significance in the chemistry of living organisms; it is broken down to release the energy needed for metabolic reactions through the process of CELLULAR RESPIRATION

3FRUCTOSE another simple sugar, this time a five-sided sugar, with one carbon forming a KETONE GROUP; this is a member of the Ketose Family

Two other five-sided sugars, found in RNA and DNA respectively, are RIBOSE andDE-OXIRIBOSE

4DISACCHARIDES = double sugars with an empirical formula of C12H22O11Two monosaccharides covalently bond during a dehydration (synthesis) reactionThe linkage formed between the 2 monosaccharides is known as a GLYCOSIDIC LINKAGEAs with all reactions, this one requires the presence of biologically active protein catalysts = ENZYMESSUCROSE= table sugar comprised of one glucose molecule and one fructose molecule

5MALTOSE disaccharide comprised of 2 glucose sub-unitsLACTOSE = milk sugar comprised of one glucose molecule and one galactose molecule EVOLUTIONARY HISTORY: Lactose Intolerance milk is a mammary product designed to sustain newborns of specific species; humans did not evolve to consume milk of other species; appear to have adapted to its consumption during one of the relatively recent glaciations; Lactose Intolerance occurs due to the absence of the enzyme LACTASE needed to digest lactose. Lactose Intolerance is more predominent in people of non-Caucasian ancestry6POLYSACCHARIDES = longer chains of covalently bonded simple sugars with the general empirical formula (CH2O)n can be very largeGLYCOGEN a common polysaccharide used by animals as a way to store glucose in the liver and muscle tissue; a highly branched chain; short-term energy storagePLANT STARCHES stored food reservesAMYLOSE = simplest plant storage starch; unbranched chain of glucose subunits; 20% of potato starch [1-4 linkages]AMYLOPECTIN = other 80% of potato starch; highly branched large polymer [1-6 linkages]7CELLULOSE the structural polymer in plants; the most abundant polysaccharide on the planetMade from BETA () GLUCOSE isomer has a difference in the position of the H and the OH on the primary carbon unit which results in every other glucose unit being invertedThe molecule does not coil, it remains linear & draws together to form cable-like MICROFIBRILS, then larger FIBRILS due to hydrogen bonding; this results in greater tensile strength & flexibility

8CELLULOSE is insoluble/indigestible to most animals; requires a specific enzyme CELLULASE to hydrolyze the moleculeTERMITES & UNGULATES (cows, etc.) have resident fauna within their intestines that secrete CELLULASE, allowing them to digest the moleculeCHITIN = 2nd most abundant polysaccharide on the planet; used by insects to form exoskeletons and by fungi for cell walls; also undigestible by most animals

9LIPIDSGreasy, oily, fat-solubleHYDROPHOBIC defined by their solubility rather than their structureGenerally NON-POLAR; so dissolve in non-polar solvents like CHLOROFORM & ETHERCan be large or small moleculesEnergy storage moleculesStructural moleculesHormones; lubricantsParts of proteins and carbohydrates

10I. TRIGLYCERIDES = Fats & OilsFATS have a higher melting point and are solid at room temperatureOILS have a lower melting point and are liquid at room temperatureBoth are comprised of 3 FATTY ACID CHAINS attached to a GLYCEROL moleculeGLYCEROL = an ALCOHOL with 3 carbons and 3 hydroxyl side groupsFATTY ACID = a hydrocarbon chain with a CARBOXYL (ACID) GROUP at one end; can be of different lengths, but commonly 14, 16, 18 or 20 carbons long; not very water soluble11TRIGLYCERIDES form through a DEHYDRATION REACTION; 3 fatty acids covalently bond with a glycerol molecule, forming ESTER LINKAGES and releasing 3 water molecules

12SATURATED FATS = triglycerides whose fatty acids contain all the HYDROGEN ATOMS possible no double bonds on the chain; all single covalent bondsHigh melting pointSolid at room temperatureMost often of animal originConsumption of these saturated fats is associated with circulatory disorder and heart disease

13UNSATURATED FAT = a triglyceride that has at least one double bond between carbons in the chain and producing a rigid point in the chain; liquid at room temperature and resists freezing; usually found in PLANTS; also found in the most exposed regions in animals that live in extremely cold environments (feet of penguin & reindeer to guard against freezing)

POLYUNSATURATED FATS = fats containing multiple carbon to carbon double bonds; multiple rigid points

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ESSENTIAL FATTY ACIDS = certain unsaturated fats we need for our cell membranes that WE CANNOT SYNTHESIZE; we are unable to synthesize double bonds in triglycerides beyond the 9th carbon in the chain; only two for humans:LINOLEIC ACID (an Omega-6 fatty acid) found in cotton seed oilALPHA-LINOLENIC ACID (an Omega-3 fatty acid) found in linseed (flaxseed) oilOther food sources for these essential fatty acids include:hemp oil/seed, shell fish, canola (rapeseed) oil, chia seeds, pumpkin seeds, sunflower seeds, leafy vegetables, & walnuts15II. PHOSPHOLIPIDS = component of the cell, and other plasma, membranesComprised of 2 FATTY ACIDS (one saturated, the other not) attached to a GLYCEROL molecule with an PHOSPHATE-BEARING COMPLEXPLASMA MEMBRANE = comprised of two PHOSPHOLIPID layers arranged tails to tails = a PHOSPHOLIPID BI-LAYER; also includes GLYCOLIPIDS (sugar lipids) and GLYCOPROTEINS (sugar proteins); the center has oily characteristics

16Phosphate head has negative charge & is HYDROPHILICThe tails are HYDROPHOBICIndividual phospholipid molecules will spontaneously assemble into BI-LAYERS and aggregate as hollow spheres called MICELLSInteraction of the polar heads & water = electrostatic attraction & hydrogen bondingHydrophobic interaction = clumping & packing together of non-polar tailsMay have been one of the mechanisms in the evolution of the first cells

17Bilayer continued . . . . . .VanDerWaals Forces = being generated by large numbers of molecules being drawn togetherPROPERTIES OF PHOSPHOLIPID BI-LAYER:Tend to self-perpetuate & be extensiveTend to close in on themselvesAutomatically repair any holes or tearsIII. WAXES = one fatty acid covalently joined by ester linkage (C-O-C) to a long chain alcoholHYDROPHOBIC even more so than fats and harderEX: beeswax; cerumen (ear wax); waxy cuticle on leaves and fruit18

IV. STEROIDS = comprised of 4 interlocking rings of carbon & hydrogen; hydrophobic & non-polar; another component of cell membranes; all steroids are derived from CHOLESTEROLCHOLESTEROL = an important nutrient with several vital functions:Used to form bile acidsA derivative is converted into Vitamin DUsed to synthesize all other steroid hormonesEstrodiols and testosterones19PROTEINSPROTEINS are the heavyweights among the molecules of life; huge MACROMOLECULES comprised of one or more POLYPEPTIDES (which are made of a linear chain of AMINO ACIDS covalently bonded by PEPTIDE BONDS enormous variation in size of the chains) PEPTIDE a short chain of amino acids joined by peptide bondsDIPEPTIDE 2 amino acids joined by a single peptide bond20PROTEINS many functions of primary importance to the structure and function of cellsSUPPORT: structural proteinsKERATIN makes up hair & nailsCOLLAGEN lends support to ligaments, tendons & skinENZYMES: bring reactants together and speed up chemical reactions; specific for one type of reaction; function at body temperature; CATALYSTSDEFENSE: ANTIBODIES are proteins; identify foreign proteins known as ANTIGENS, to prevent these antigens from destroying cells, causing disease & thus upsetting homeostasis

21TRANSPORT: plasma membrane contains CHANNEL & CARRIER PROTEINS allow substances to enter and exit cells. Other proteins transport molecules in the blood of animalsHEMOGLOBIN huge globular 4 level protein pigment on RBCs that transports O2 in the bloodHORMONES: regulatory proteins; intercellular messengers that influence the metabolism of cellsINSULIN regulates level of glucose in blood & cellsHUMAN GROWTH HORMONE determines height of individualMOTION: contractile proteins ACTIN & MYOSIN allow parts of cells to move & cause muscles to contract; enables animals to move from place to place22TWO GENERAL CATEGORIES OF PROTEIN SHAPEGLOBULAR: folds spontaneously into compact globs usually has a large preponderance of ALPHA HELIX sections in its structureENZYMES, HORMONES & ANTIBODIESFIBROUS: remains linear, but zig-zags or fan-folds; occurs in MUSCLES, LIGAMENTS & TENDONS; preponderance of BETA-PLEATED SHEET segmentsCOLLAGEN makes up most of the structure of ligaments and tendons and is the most common protein in the vertebrate body

23AMINO ACIDS: basic building blocks of PROTEINSThere are 20 PRIMARY AMINO ACIDS Additional secondary amino acids are derived from the primary amino acidsAll of them have the same basic structure

24Amino Acids continued . . . .Readily ionize in standard physiological conditions; carboxyl group gives off a proton and the amine group takes on a proton so it has both a (+) and a (-) chargeThe R-GROUPS are where the 20 amino acids differ; their structure and properties affect proteins shape8 NON-POLAR R-GROUPS: hydrophobic - mainly hydrocarbons that cluster together in a water environment7 POLAR R-GROUPS: hydrophilic form HYDROGEN BONDS with water and with other polar R-groups5 R-GROUPS IONIZE WITH WATER and thus bear additional (+) and (-) charges(+) charged amino acids within a protein will interact with one another to form IONIC BONDS25

26CONFORMATION: a proteins specific 3-dimensional shape; determined by amino acid content and their various interactionsMany proteins work through RECOGNITION & BONDINGRECOGNITION = by proteins shapeBONDING = of substance & protein at a particular site or locationPOLYPEPTIDES: the carboxyl group of one amino acid linked in a peptide bond to the amine group in the next amino acidN-TERMINAL = beginning of peptide chain; free amineC-TERMINAL = end of peptide chain; free carboxyl27FOUR LEVELS OF PROTEIN STRUCTURE1-PRIMARY determined by the number, type & order of amino acids in the chain determined by genetic sequence2-SECONDARY occurs spontaneously as the protein forms; EITHER . . . ALPHA HELIX: a right-hand coil formed as a result of hydrogen bonding along strand; number of bonds leads to stable configuration; occurs in GLOBULAR PROTEINSBETA SHEETS: back & forth folding; maintained by hydrogen bonds between adjacent strands; principally found in FIBROUS PROTEINS28

Levels of Protein Structure continued . . . .3TERTIARY: highly specific looping & folding due to interactions of various R-Groups; each unique; tertiary structure is rigidly set & determined by the primary structure4 forces influence foldingHYDROPHOBIC INTERACTIONS among non-polar amino acidsHYDROGEN BONDS between adjacent polar R-GroupsIONIC ATTRACTIONS between oppositely charged R-GroupsCOVALENT BONDING when 2 cystine amino acids form DISULFIDE LINKAGES29Levels of Protein Structure continued . . . .4QUATERNARY: when 2 or more polypeptides join to form the finished proteinHEMOGLOBIN: comprised of 4 poly peptides 2 pairs a virtual giant among proteins

30Proteins can readily be DENATURED = have their conformation (and thus their effectiveness) altered by a chemical or physical agentLoses biological functionCauses old bonds to break and new bonds to form randomlyHEAT (egg white ALBUMEN)INTENSE COLD usually reversibleAlkalinity & ACIDITY

Cant unboil an egg

31STRUCTURAL PROTEINS: maintain the physical form of organismsINTRACELLULAR: within cellsKERATIN fills the growing cells of hair, feathers, claws, nails, horns, antlers & scales; dead cell layers are pushed out by growing cells beneath

EXTRACELLULAR: outside of cellCOLLAGEN long, fibrous molecules wound together to make long fibers; 25% of protein in humans ; tendons, ligaments & muscles

32ELASTIN gives elasticity to connective tissue - EARS & SKIN loses elasticity with aging; wrinkling; the pinch test

CONJUGATED PROTEIN: one that contains chemical components other than amino acids; generally named for the added chemical componentHEMOPROTEINS: hemoglobin; contains HEME GROUPS (iron-containing nitrogen ringsLIPOPROTEINS: possesses lipid componentsGLYCOPROTEINS: possesses carbohydrate componentsPHOSPHOPROTEINS: possesses phosphate components33NUCLEIC ACIDSDNA = Deoxy-Ribonucleic Acid = molecular core of life contains GENES (units of heredity) that specify the types of proteins the organism produces - its DOUBLE-STRANDED & SELF-REPLICATINGRNA = Ribonucleic Acid = a related molecule - its SINGLE-STRANDED & is vital in translating information from DNA into assembled proteins

34NUCLEOTIDE = the subunit of which nucleic acids are comprised; includes a 5-CARBON SUGAR (ribose or deoxyribose), a PHOSPHATE GROUP & one of 4 NITROGENOUS BASESNITROGENOUS BASE can be either a single (PURINES) or double ringed (PYRIMIDINES) molecule (2 of each)ADENINE - purineGUANINE - purineCYTOSINE - pyrimidineTHYMINE - pyrimidineURACIL - pyrimidine (only in RNA)

35NUCLEOTIDES form polymer chains by covalently bonding between the sugar of one molecule and the phosphate group of the nextIn DNA, the polymer chains are drawn together and form WEAK HYDROGEN BONDS between the nitrogenous bases in one with the nitrogenous bases in the other. They then are spontaneously twist into a DOUBLE HELIXCHARGAFFS RULES:The amount of A, T, G & C in DNA varies from species to speciesIn each species, the amount of A = T, and the amount of C = G

36ENZYMES -aseORGANIC CATALYSTS accelerates the rate of chemical reactions by lowering the ACTIVATION ENERGY necessary for the reaction to take placeACTIVATION ENERGY the minimum energy sufficient to form new bonds

A catalyst is not changed by the reaction & can be used over & over againMETABOLISMS = chemical reactions that occur in biological systems37CATABOLISM = breaking down of substancesANABOLISM or SYNTHESIS = formation of new products

CHEMICAL EQUALIBRIUM: when the rate of the forward reaction = the rate of the reverse reaction; therefore no net production of either reactants or products

38ENZYMES are specific for particular reactions because of shapeINDUCED-FIT MODEL (formerly LOCK &KEY MODEL) of enzyme action ACTIVE SITE on enzyme binds with SUBSTRATE (substance upon which the enzyme acts) MOLECULE due to SHAPE, POLARITY or other characteristics of the active site Enzyme then changes its shape slightly & lowers activation energy of reaction

39Enzymes operate at an optimum temperature (37C for humans) and pH (varies by species & area in body)DENATURING destroys enzymes shape and therefore its functionSometimes ELASTIC, as with freezingMainly permanent, as in spiking a fever above 104.5FATP Common source of ACTIVATION ENERGY for metabolic reactions; break high energy bonds between SECOND & THIRD phosphate groupsCO-FACTORS = non-protein molecules that assist enzyme actionCOENZYMES: organic co-factors such as VITAMINSINORGANIC CO-FACTORS: often metal ions (Fe++)40REGULATING ENZYME ACTIONALLOSTERIC ENZYMESTwo types of ACTIVE SITESFor SubstrateFor ALLOSTERIC EFFECTOR presence or absence of either activates or inhibits enzyme actionFEED-BACK INHIBITION = end product of reactions acts as allosteric effectors to inhibit enzyme and shutdown reactionCOMPETITIVE INHIBITION = substance inhibits enzyme by occupying its active site this displaces the substrate41