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2011-12-20 14:30:54
organic biochemistry

Organic and Biochemistry Final Lab Exam Review
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  1. Draw and name the four possible structural formulas with the molecular formula C3H6Cl2
    • 1,1-Dichloropropane
    • 1,2-Dichloropropane
    • 1,3-Dichloropropane
    • 2,2-Dichloropropane
  2. Draw and name the two constitutional isomers for C4H10

    2-Methylpropane (isobutane)

  3. Draw and name the three constitutional isomers of C3H8O
    • 1-Propanol
    • 2-Propanol
    • Ethyl methyl ether
  4. Draw the chair conformation for cyclohexane. Show the hydrogens and label which are equatorial and which are axial.

    Red is axial
  5. What are the bond angles for methane? ethylene? acetylene?
    Methane - Single Bond - 109.5 degrees

    Ethylene - Double Bond - 120 degrees

    Acetylene - Triple Bond - 180 degrees
  6. Draw the cis and trans structures for 2-hexene. What type of isomers are these compounds?
    • Remember the "2" in 2-hexene means to place the double bond on the 2nd carbon.

    The isomers are Stereoisomers (same connectivity but different orientation in space).
  7. Is toluene more soluble in water or methylene chloride? Why?
    Toluene is not soluble in water because of the benzene ring. Toluene is soluble in methylene chloride because "Like Dissolves Like" and both toluene and methylene chloride are organic.

    Remember: Most organics are insoluble in water but soluble in other organics and most burn or decompose quickly.
  8. Describe what happens when bromine is added to an alkene. Write a balanced equation.
    Unsaturated aliphatic hydrocarbons react rapidly with Br2 and with KMnO4 to produce distinct color changes. Saturated and aromatic hydrocarbons, on the other hand, require much more vigorous conditions. Thus, a compound that gives a positive test (clear) w/ Br2 and/or KMnO4 must be unsaturated, and a compound that gives a negative test (stays red) result must be saturated -or- aromatic.

    • A positive reaction: C=C becomes 1,2-Dibromo-ethane and the solution turns from red (bromine) to clear
  9. Describe what happens when potassium permanganate (KMnO4) is added to an alkene. Write the equation.
    KMnO4 may be used as an oxidizing agent to differenciate between alkanes and alkenes.

    The alkene's double bond changes to a single bond and OHs bond to the carbons that used to hold the double bond.

    A cyclohexane would not react.
  10. Which will give the most soot when ignited? Cyclohexane, cyclohexene, toluene, or ethanol?
    • Saturated hydrocarbons burn cleanly.
    • Unsaturated and aromatic hydrocarbons burn with lots of soot

    Toluene, an aromatic hydrocarbon, will give the most soot when ignited.

    Ethylene a saturated hydrocarbon will give the least amount of soot.
  11. Are hydrocarbons more or less dense than water?
    Hydrocarbons are less dense than water.
  12. How would you determine the mass of an ethanol solution if 5.00mL had a density of 0.816 g/mL.
    0.816 g/mL x 5.00 mL = 4.08g

    Note mL cancelled out.

    • D = M/V therefore, M = D x V
  13. What is the proof of an ethanol solution that is 95% ethanol? How do you figure this out?
    The proof is two times the alcohol percentage... 190 proof

  14. Simple Distillation
    The technique of heating a liquid to its boiling point, condensing the vapors and collecting the condensate (distillate).

    Works best with liquids that have a 100 degrees celsius or greater difference in boiling points.
  15. Fractional distillation
    "Repeated distillation" in the form of a fractionating column to increase the surface area within the distillation aparatus.

    Fractional distillation works better than simple distillation for separating liquids that have boiling points which are less than 100 degrees celsius apart... even those that only within a few degrees of each other.
  16. Steam Distillation
    Steam distillation is a technique used for the vaporization of volatile, water-insoluble compounds with steam.

    The steam for the distillation is generated from boiling water in the presence of the plant material. The theoretical basis of the technique is that a mixture of immiscible liquids will boil when their combined vapor pressures equal the opposing atmospheric pressure. Thus, the volatile organic compounds in a mixture will distill together with the water vapor and leave the nonvolatile compounds behind.

    We obtain essential oils by boiling the plant material, collecting the steam with the essential oil within, and then isolating the oil by extracting it into an organic solvent such as ether, and then evaporating the solvent.
  17. Azeotrope
    Two or more liquids form a constant boiling mixture of fixed composition.

    The components of such a mixture can not be distilled.
  18. Is it possible to get a good separation of pentane and heptane with simple distillation? Why or why not?
    • Boiling Point of Pentane = 36 degrees celsius
    • Boiling Point of Heptane = 98 degrees celsius

    No. Simple distillation works best when boiling points are 100 degrees celsius or more apart.
  19. Why are the components of essential oils from plants not water soluble?
    Possibly because they tend to have high molecular weights that outweigh the solubility of their polar parts and also because they contain aromatic rings that are not soluble in water.
  20. On a TLC plate the solvent moved 4.3 cm and a component of a mixture was located 2.5 cm from the spotting line. Calculate the Rf of this component.
    Rf = spot divided by solvent

    2.5 / 4.3 = 0.58
  21. In general, does a non-polar or polar substance move faster on a TLC plate like those used in lab?
    Non-polar moves faster.

    Ordinarily, nonpolar compounds are more mobile than polar compounds.

    Also, in general, the more polar a solvent is, the more effective it is at eluting (carrying) both polar and nonpolar compounds.
  22. Write the equation for the preparation of aspirin from salicyclic acid and acetic anhydrived. [Use Structures]
    Label the carboxylic acid, phenol, anyhydride, and ester functional groups.
  23. What is the structure of a nylon molecule formed from ethanedioic acid and 1,2-diaminoethane? Name this nylon. What is the side product formed in this reaction?
  24. What is a chromophore?
    A chromophore is the part of a molecule responsible for its color.

    A chemical group capable of selective light absorption resulting in the coloration of certain organic compounds.

    The presence of certain unsaturated functional groups, called chromophores, nearly always results in color.

    Common examples include retinal (used in the eye to detect light), various food colorings, fabric dyes (azo compounds), pH indicators, lycopene, β-carotene, and anthocyanins.

    Common chromophoric groups include carbonyl (C=O), azo (N=N), nitro and aromatic polyenes.
  25. What is an auxochrome
    Auxochromes intensify or augment color when present in a molecule with a chromophore, although they usually confer no color themselves.

    Any radical or group of atoms that intensifies the color of a substance

    Structurally, such groups possess non-bonded electron pairs, usually in the form of oxy or amino groups. As illustrations of these structural relationships, benzene and phenol are colorless, but nitrobenzene is pale yellow, and p-nitrophenol, which contains an auxochromic hydroxy group, is bright yellow.
  26. What color is methyl orange at various pHs?
    Methyl orange is a pH indicator frequently used in titrations of acids...

    More Acidic (below 3.1) is Red

    More Basic (above 4.4) is Yellow

    • In Lab pH 5.0 HCL solution Deep Red
    • In Lab pH 11 NaOH solution Deep Orange
  27. Draw the following molecules.
    Which molecules are chiral? Mark the stereocenters.
    2-chlorobutane, 3-methylpentane, 2-pentanol
    • 2-pentanol



  28. Draw a Fischer projection for D-glucose and for L-glucose.
    Draw a disastereomer of D-glucose.
    Draw a Haworth structure for D-Glucose
    • Enantiomers, the right- and left-handed forms of molecules, are defined as nonsuperimposable mirror images.

    • Diasteromers are defined as stereoisomers that are not enantiomers. That is, if two molecular structures have all the same connections but they differe in the three-dimensional spatial orientations of their substituent group such that they are not mirror images of one another, then they are diastereomers.
  29. What terms describe the relationship between D-glucose and L-glucose molecules?
    In general, D-configuration refers to a Fischer projection in which the non-hydrogen group is on the right.

    Note that D and L are means to describe the configurations of chiral centers. These are not to be confused with d and l, which describe the optical rotation properties of the compounds.
  30. Dextrorotatory
    The clockwise (to the right) rotation of the plane of polarized light in a polarimeter.
  31. Levorotatory
    The counterclockwise (to the left) rotation of the plane of polarized light in a polarimeter.
  32. Optically active
    Showing that a compound rotates the plane of polarized light.
  33. Racemic
    A mixture of equal amounts of two enantiomers.

    Enantiomers are stereoisomers that are nonsuperposable mirror images; refers to a relationship between pairs of objects.
  34. Epimers
    Epimers are diastereomers that differ in configuration of only one stereogenic center.

    In chemistry, epimers are diastereomers that differ in configuration of only one stereogenic center. Diastereomers are a class of stereoisomers that are non-superposable, non-mirror images of one another.

    The sugars α-glucose and β-glucose are epimers. In α-glucose, the -OH group on the first (anomeric) carbon is in the direction opposite the methylene group on carbon C-6 (in the axial position). In β-glucose, the -OH group is oriented in the same direction as the methylene group (in the equatorial position). These two molecules are both epimers and anomers.
  35. The Molisch Reagent is used as a general test for ____.
    A positive result is indicated by _____.
    The Molisch Reagent is used as a general test for any carbohydrate larger than a tetrose.

    A positive result is indicated by a dark color (usually brown or purple).
  36. The Benedict's Reagent is used as a general test for _____.
    A positive result is indicated by _____.
    The Benedict's Reagent is used as a general test for reducing sugars.

    Formation of a voluminous red-orange dispersion is indicative of a reducing sugar.
  37. The Barfoed's Reagent is used as a test for _____.
    A positive result is indicated by _____.
    The Barfoed's Reagent differentiates a reducing monosaccharide from a reducing disaccharide.

    A positive test for reducing monosaccharide is indicated by the formation of a reddish precipitate within three minutes.

    Barfoed's Test is a chemical test used for detecting the presence of monosaccharides. It is based on the reduction of copper(II) acetate to copper(I) oxide (Cu2O), which forms a brick-red precipitate.

  38. The Bial's Reagent is used as a test for _____.
    A positive result is indicated by _____.
    The Bial's Reagent differentiates a pentose from a hexose.

    • A pentose is typically indicated by a greenish color.
    • A hexose is indicated by a brownish color.
  39. The Seliwanoff's Reagent is used as a test for _____.
    A positive result is indicated by _____.
    The Seliwanoff's Reagent differentiates aldohexoses and ketohexoses.

    This test is based on the fact that, when heated, ketoses are more rapidly dehydrated than aldoses.

    • The dehydrated ketose then reacts with the resorcinol to produce a deep cherry red color.
    • Aldoses may react slightly to produce a faint pink color.
  40. The iodine reagent is used as a test for _____.
    A positive result is indicated by _____.
    • The iodine reagent is used as a test for starch amylose.
    • A positive result is indicated by a dark blue/black color.

    • Starch amylopectin does not give the color, nor does
    • cellulose, nor do disaccharides such as sucrose in sugar, nor glycogen.
  41. Write the saponification reaction of a triglyceride (made from myristic acid, oleic acid, and linolenic acid) with NaOH.
    Example of Saponification:

  42. What causes insoluble scum to form when soap is used in hard water?
    Soaps form water-insoluble salts when used in water containing Ca(II), Mg(II), or Fe(III) ions (hard water).

    2CH3(CH2)14COO-Na+ + Ca2+ --> [CH3(CH2)14COO-]2Ca2+ + 2Na+

    A sodium soap (soluble in water as micelles) plus Ca2+ results in a Calcium salt of a fatty acid (insoluble in water).
  43. Describe how soap can remove both grease and water-soluble particles from clothing.
    When soap and "dirt" are mixed together in water the nonpolar hydrocarbon inner parts of the soap micelles "dissolve" the nonpolar substances. In effect, new soap micelles form, with the nonpolar dirt molecules in the center. In this way, nonpolar organic grease, oil, and fat are "dissolved" and washed away in the polar wash water.
  44. Micelles - soap - cleaning
    Soap owes its remarkable cleansing properties to its ability to act as an emulsifying agent.

    Because the long hydrocarbon chains of natural soaps are insoluble in water, soap molecules tend to cluster in such a way as to minimize contact of their hydrocarbon chains with surrounding water molecules. The polar carboxylate groups, by contrast, tend to remain in contact with the surrounding water molecules. Thus, in water, soap molecules spontaneously cluster into micelles that surround 'dirt' and wash away in the rinse water.
  45. Would a saturated or unsaturated lipid require more bromine reagent? Why?
    • Bromine (Br2) reacts with double bonds by turning them into single bonds. Unsaturated lipids have double bonds and saturated lipids do not. Thus bromine would not react with saturated lipids (staying reddish brown) but would react with unsaturated lipids (losing its color).
  46. Is soap or detergent a better emulsifying agent? Why?
    Synthetic detergents are a better emulsifying agent than soap because because detergent has a sulfonate (--SO3-) group instead of a carboxylate (--COO-) group. Calcium, magnesium, and iron salts of alkylsulfonic acids (R-SO3H) are much more soluble in water than comparable salts of fatty acids.
  47. The Biuret Test is used for _____.
    A positive result is indicated by _____.
    The Biuret test is a general test for any polypeptide larger than a dipeptide.

    Formation of a violet (occasionally pink) color is a positive test.
  48. The Ninhydrin Test is used for _____.
    A positive result is indicated by _____.
    The Ninhydrin Test is a general test for free amino acids.

    Formation of a dark violet color is a positive test.
  49. The Xanthoproteic Test is used for _____.
    A positive result is indicated by _____.
    The Xanthoproteic Test is a diagnostic test for the presence of aromatic side-chains.

    Formation of a dark orange-yellow color is a positive test.
  50. What effect do each of the following have on protein? Heat, acid, alcohol, lead.
    Each may denature the protein molecule.

    For example, heat cleaves hydrogen bonds, so boiling a protein solution destroys the alpha-helical and beta-pleated sheet strucure.

    Acids may affect salt bridges thereby changing the formation/structure of the protein.

    Alcohols may cause coagulation.

    • Lead denatures proteins by attacking the --SH groups.
  51. What is meant by an inhibitor of an enzyme?
    Any process that reduces enzymatic activity is known as inhibition.

    Inhibition results when the active site is blocked by interaction with a molecule that is structurally related to the proper substrate.

    Inhibition may be competitive or non-competitive and may result in partial or total loss of activity.
  52. Draw a diagram to show what is meant by the in reference to an enzyme and substrate.
  53. How do the following factors influence enzyme activity?
    Concentration, temperature, pH.
    • a) Substrate concentration
    • Saturation Curve. The rate does not increase continuously because a point is reached after which the rate stays the same even if we increase the substrate concentration further. At the saturation point, substrate molecules are bound to all available active sites of the enzymes.

    • b) Enzyme Concentration
    • The rate increases linearly because the molar concentration of enzyme is almost always much lower than that of substrate.

    • c) Temperature
    • Most enzymes have an optimal temperature of 37 degrees C. If we start below this temp and increase the temp the reaction rate will increase. However, if we get too hot we may alter the enzyme surface and the reaction rate will decrease.

    • d) pH
    • The curve is the same as with temps. There is an optimal pH (7.3 for humans). Too high or low decreases the reaction rate however within the narrow range of optinum increases...