Macromolecule Scramble

Intro to Macro moleculesBiochemistry

Molecular BiologyThe study of the structure and functioning of biological moleculesClosely linked with biochemistryStructures of molecules closely linked with function of the moleculeMetabolismThe sum of all the biochemical reactions that happen in the bodyThe breaking down of molecules in order to obtain ATP that will then be used to build other molecules needed for life

What were the first molecules?Chemical evolution occurred billions of years ago Thousands of carbon based molecules emerged from the more simple molecules that existed on early EarthRaw ingredients on earth that were used to create life:Carbon dioxide (CO2)Hydrogen gas (H2)Water (H2O)Nitrogen gas (N2)Ammonia (NH3)Hydrogen sulfide (sulphide) (H2S)Energy source (electrical discharge lightning)All these led to the first Amino acidswhat is the structure of AA?AA led to first proteins=LIFE4 most abundant elements in living organismsHydrogenCarbonOxygenNitrogenThey account for 99% of all atoms found in living thingsCarbon however, is the most importantwhy do you think so?

CarbonThe element of LIFE!Found in all living organisms! We are always looking for carbon based life formsOrganic molecules: molecules that contain carbonC6H12O6, CO2, CH4Some molecules are made of just CARBON and HYDROGENwe call these HYDROCARBONSThese are important in FUEL (aka GASOLINE!!)Many organic molecules, such as fats, have hydrocarbon componentsHydrocarbons can undergo reactions that release a large amount of energyInorganic molecules: molecules that do not contain carbonH2O, NH3, O2

LE 4-4Hydrogen(valence = 1)Oxygen(valence = 2)Nitrogen(valence = 3)Carbon(valence = 4)6Structure of CarbonStructureValence electrons: 4How many bonds can carbon make with other atoms?4: single, double, or tripleas long as it has 4 lines touching itThis makes carbon a versatile atomit can make long chains of carbons, branched carbon structures, even ring structures with itself

Drawing and numbering carbon structuresStart with the carbon that is in a carboxyl functional groupthat is #1 and then follow sequentiallyIn ring structures, the C for carbon may be omittedit is understood that where ever there are vertices, there is a carbon atom Hs for hydrogen are also left off for simplicity

LE 4-5LengthEthanePropaneButane2-methylpropane(commonly called isobutane)BranchingDouble bondsRings1-Butene2-ButeneCyclohexaneBenzene9Some important words to knowMoleculeGroup of covalently bonded atomsMacromoleculelarge molecules composed of thousands of covalently connected atomsFunctional GroupsGroup of atoms within a molecule that interact in PREDICTABLE waysPolar, non-polar, acidic, basic, charged (+/-)Hydroxyl groupCarbonyl group Carboxyl groupAmino groupSulfhydryl groupPhosphate group

Two REALLY ImportantMolecules with Phosphate GroupsATPDNA (nucleotide)

LE 4-10aaSTRUCTURE(may be written HO)NAME OF COMPOUNDSAlcohols (their specific namesusually end in -ol)Ethanol, the alcohol present inalcoholic beveragesFUNCTIONAL PROPERTIESIs polar as a result of theelectronegative oxygen atomdrawing electrons toward itself.Attracts water molecules, helpingdissolve organic compounds suchas sugars (see Figure 5.3).14

LE 4-10acSTRUCTURENAME OF COMPOUNDSCarboxylic acids, or organic acidsEXAMPLEHas acidic properties because it isa source of hydrogen ions.Acetic acid, which gives vinegarits sour tasteFUNCTIONAL PROPERTIESThe covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,Acetic acidAcetate ionIn cells, found in the ionic form,which is called a carboxylate group.15

LE 4-10baSTRUCTURENAME OF COMPOUNDSAmineEXAMPLEBecause it also has a carboxylgroup, glycine is both an amine anda carboxylic acid; compounds withboth groups are called amino acids.FUNCTIONAL PROPERTIESActs as a base; can pick up aproton from the surroundingsolution:(nonionized)Ionized, with a charge of 1+,under cellular conditionsGlycine(ionized)16

LE 4-10bcSTRUCTURENAME OF COMPOUNDSOrganic phosphatesEXAMPLEGlycerol phosphateFUNCTIONAL PROPERTIESMakes the molecule of which itis a part an anion (negativelycharged ion).Can transfer energy between organic molecules. 17What are macromolecules made of?A polymer is a long molecule consisting of many similar building blocks called monomersPoly=manyMono=oneThink of a beaded bracelet.Large variety of polymers but there are less than 50 like the alphabetlots of words, only 26 lettersPolymerization: THE PROCESS OF MAKING A LARGER MOLECULE BY PUTTING TOGETHER SMALLER MOLECULESThree of the four classes of lifes organic molecules are polymers:CarbohydratesProteinsNucleic acids

***Lipids/fats are not polymers but they are still macromolecules

Brief Overview of 4 MacromoleculesCarbohydratesMonomer: monosaccharaides and disaccharidesPolymer: polysaccharides aka complex carbohydrates (Starches, cellulose)ProteinsMonomer: Amino acidsPolymer: Polypeptide Chain (PROTEINS)Nucleic AcidsMonomer: NucleotidePolymer: Nucleic Acids (DNA and RNA)Lipids, fats, oils and steroidsMonomer: NONEPolymer: NONE

Making and Breaking PolymersPolymerization: making polymersDehydration/condensation ReactionDehydrate means water lossWhen a water molecule (H-OH) is released to join a monomer to another monomerHydrolysisHydro- waterLysis- to break downDef: to break apart or disassemble a polymer by adding water (H-OH)

LE 5-2Short polymerUnlinked monomerDehydration removes a watermolecule, forming a new bondDehydration reaction in the synthesis of a polymerLonger polymerHydrolysis adds a watermolecule, breaking a bondHydrolysis of a polymerPolymerization (polymerisation)Process of putting together many monomers to make a larger polymerExamples of common polymers:Natural:RubbercelluloseIndustrially produced:PolyesterPolythenePolyvinyl chloride (PVC)NylonAll of the above are carbon based subunits containing thousands of carbon atoms joined end to end

CarbohydratesDivided into 3 main groups:Monomer: Monosaccharide or DisaccharidePolymer: PolysaccharideLink between monomers is called: Glycosidic LinkageFormed by a dehydration/condensation reactionAlways have Carbon, Hydrogen, and OxygenCx(H2O)yCommon name: sugarEnd with suffix -oseFunction: Energy/fuel, structure, storageGLUCOSE!!!! What all cells need for energy

MonosaccharidesSugarsDissolve easily in water to form sweet solutionsLarge carbs (starches and cellulose) do not dissolve Think about your towels and clothes, duh!General formula: (CH2O)nConsist of single sugar molecule (hence mono)Classified according to # of carbon atoms in each moleculeTrioses (3C)Pentoses (5C)Ribose & deoxyriboseHexoses (6C)Glucose, fructose, galactoseEx: Glucose, Fructose, Galactose2 major Functions: 1. Energy source in respiration (b/c of large # of C-H bonds that can be broken to release ATP)2. Important building blocks for larger molecules

PentosesHexosesMolecular and structural formulasMolecular formulas show the # of each atom in a molecule but not how they are arrangedMolecular Formula for hexoses: C6H12O6Both glucose and fructose have the same molecular formula C6H12O6Structural formulas are used to show the arrangements of the atomsRing structuresPentoses and hexoses are a chain of carbon atoms that are long enough to close up on each other and form rings (occurs in AQUEOUS environment)This ring structure is more stable than a chain, therefore atoms in these molecules stay inn rings not chainsGlucose: carbon #1 joins the oxygen attached to carbon #5carbon #6 is not part of the ring

GlucoseC6H12O6Hydroxyl groups on carbon #1 can either be above the plane or below the planeDifferent spatial arrangement of atoms in the same molecule are called ISOMERS These isomers of glucose are important in the formation of polysaccharides: starch, cellulose and glycogenHydroxyl group on C-2 is always below the plane, and the following carbon atoms alternateAlpha Glucose hydroxyl group is BELOW the ring planeBeta GlucoseHydroxyl group is ABOVE the ring plane

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Alpha vs Beta glucose

Dissaccharidesformed by glycosidic linkagejoin together two hydroxyl groups by a process called CONDENSATION (dehydration)literally lose a water moleculeHYDROLYSIS is the opposite of condensation rxnit causes the breaking of a glycosidic linkageoccurs during the digestion of disaccharides and polysaccharidesBoth reactions controlled by enzymesCommon disaccharides: Maltose and SucroseLactose, Maltose and Sucrose

Functions of Monosaccharides & DisaccharidesGood sources of energy for living thingsUsed in respiration ATPDue to solubility, this is the form carbohydrates are transported through an organisms bodyAnimals glucose is dissolved in blood plasma for transportPlants sucrose is transported in phloem sapReducing vs.Non-reducing SugarsReducing sugarsAll monosaccharides (glucose)Some disaccharides (maltose)Carry our reduction reaction (donates electrons) and thus become oxidisedDisaccharide SUCROSEDo NOT carry our reduction reactions

Non-reducing sugars

Reducing Sugar TestBenedicts Solution/ReagentBlue colored solutionCopper (II) sulfate in an alkaline solutionIn the presence of reducing sugars, copper (II) sulfate (contains copper II ionsCu2+ ) becomes reduced to insoluble red-brown copper-oxide (contains copper ICu1+ ) it loses 1+ charge because it has gained an electron from the reducing sugarRed-brown copper oxide is visible as a brick red precipitateReducing sugar + Cu2+ oxidized sugar + Cu1+ BLUE RED/BROWN

Reducing Sugar Test Continued Reducing sugar + Cu2+ oxidized sugar + Cu1+ BLUE RED/BROWNIntensity of red color is related to concentration of reducing sugarBenedicts solution is added to solution being testedMixture is heated in warm water bathIn presence of reducing sugar, gradual color change occursGreen yellow orange red/brownMust use EXCESS of benedicts solution to ensure relationship between color intensity on concentration of reducing sugar2 ways to measure concentrations:Compare to set of colour standards previously made with known reducing sugar concentrationsUse a colorimeter to measure concentrations more precisely

Test for non-reducing sugar (sucrose)Benedicts test would yield NEGATIVE result (no color change, solution remains blue)Testing a non-reducing sugarFirst break disaccharide a into monosaccharides using ACID HYDROLYSIS (use hydrochloric acid and a warm water bath)Benedicts requires ALKALINE environment, so after heating sugar/HCL mixture, add sodium hydroxide in excess to NEUTRALIZETHEN, add Benedicts reagent to neutralized solution and heatResults:Blue to brick red precipitate = non-reducing sugar presentNo color change for either test = no sugars present at allMixture of reducing and non-reducing sugars will yield a heavier precipitate in the non-reducing sugar test than in the reducing sugar test previously described

Reducing Sugar TestSafetyEquipmentHow to read syringeRange of Solutions of different concentrations0% water20%solution50% solution100% solution

Practice Question Set 2 (6 questions)