SEMINAR QUESTIONS - ?· SEMINAR QUESTIONS (Seminar 2-19) ... glucose and stearic acid (CH3(CH2)...

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Transcript of SEMINAR QUESTIONS - ?· SEMINAR QUESTIONS (Seminar 2-19) ... glucose and stearic acid (CH3(CH2)...

  • Department of Medical Biochemistry and Biophysics (MBB) Biomedicine programme (candidate) General and Organic Chemistry (AOK) HT13


    (Seminar 2-19)

  • KAROLINSKA INSTITUTET Department of Medical Biochemistry & Biophysics Biomedical program (Candidate): General and organic chemistry SEMINAR 2 Lab procedures 1. What do you need to keep in mind when you choose glassware for your synthesis? 2. A student performs a vacuum distillation using a water aspirator (strlpump) to create the

    vacuum. A sudden drop in water pressure leads to back-splashing of water - the experiment is ruined and the student has to start from the beginning. He suddenly realizes that he forgot to incorporate a piece of equipment in the apparatus that could have prevented the disaster. What is it?

    3. How does one recrystallize the raw product from a synthesis? 4. Why does one sometimes need to perform a vacuum distillation? What boiling point does a substance have at 10 mm HG when it boils at 250 C at normal air

    pressure? 5. What is the purpose of a TLC and how does it work? When is it performed? How is the mobile phase chosen? How is the result interpreted? 6. When does one use desiccator grease (vakuumfett)? When is it not appropriate to use it? 7. Why are anti-bumping granules used? How do they work? Does a magnetic stirrer work equally well? 8. How do you measure up 10 g of a liquid? Useful literatur: Labkompendium pages 21-30, 93-95, 112-119 Norin Elementr kemisk laboratorieteknik

  • KAROLINSKA INSTITUTET Department of Medical Biochemistry & Biophysics Biomedical program (Candidate): General and organic chemistry SEMINAR 3 Atom structure and chemical bonds F&F 1.1, 1.2, 1.4, 1.13, 2.9, 2.24 1. Which of the following molecules are dipoles: chlorine gas, hydrogen chloride,

    chloroform (trichloromethane), carbon tetrachloride (tetrachloromethane)? Explain your answer.









    O OH

    A B


    HO OH


    2. Which of the following molecules has a dipole moment? Indicate the direction of each.

    OH 3. H2 forms a stable diatomic molecule but He2 does not. Why is that? Explain with the

    help of molecular orbitals! 4. Why does the electron negativity of the elements increase when one goes up/to the

    right in the periodic system? 5. What kind of hybridization do you expect for each carbon atom in: A) vitamin C

    (ascorbic acid), B) aspirin (acetylsalicylic acid)? 6. A lab technician accidentally mixed two substances, glucose and stearic acid

    (CH3(CH2)16COOH). How can the substances easily be separated again?

  • KAROLINSKA INSTITUTET Department of Medical Biochemistry & Biophysics Biomedical program (Candidate): General and organic chemistry SEMINAR 4 Structural isomerism, alkanes F&F 2.16, 2.33, 3.1, 3.5, 3.7, 3.9 1. Name the following compounds!

    CH2 C CH2 CH2 CH3

    CH CH










    a) b)

    CH3 CH3

    CH3 C C C CH3


    CH3c) d)

    Ce) f)

    Ig) h)


    OH Br


    O Hi)

  • H3C CH

    H2C C CH3




    2. Identify the carbon atoms in the following molecule as primary, secondary, tertiary or quaternary.

    3. Draw structural formulas for 4 compounds that have the empirical formula C3H6O! 4. Oxaloacetic acid, an important intermediate in food metabolism, has the formula C4H4O5 and

    contains three C=O bonds and two O-H bonds. Propose two possible structures. 5. What does trivial name mean? Give the trivial names for the following compounds: a) 2-

    propanone; b) 2-propen-l-ol; c) propanal; d) propanoic acid; e) 2-propenoic acid; f) ethanoic acid!

  • KAROLINSKA INSTITUTET Department of Medical Biochemistry & Biophysics Biomedical program (Candidate): General and organic chemistry SEMINAR 5 Stereo isomerism, conformations F&F 4.2, 4.3, 4.6, 4.40, 4.47, 4.7, 4.8, 4.9, 4.33 1. Rank the substituents in each of the following sets according to the Cahn-Ingold-Prelog

    rules: a) H, -OH, -CH2CH3, -CH2CH2OH b) CO2H, -CO2CH3, -CH2OH, -OH c) CN, -CH2NH2, -CH2NHCH3, -NH2



    2. Alanine, an amino acid found in proteins, is chiral. Draw the two enantiomers of alanine using the standard convention of solid, wedged, and dashed lines. Which has R-configuration and which has S-configuration?

    Alanine 3. Build models of (2Z,6Z)-2,6-nonadiene and (2E,6E)-2,6-nonadiene.

    Compare the lengths of the molecules which isomer is longer and why? 4. Build a model of (2R,3R)-2,3-dihydroxybutyric acid. Indicate the stereo chemistry of the

    molecules using the Fischer system! 5. Build models of (2R,3R)-tartaric acid and (2R,3S)-tartaric acid. Which of the molecules has

    a symmetry plane? What is meant with meso-form? How many stereoisomers of tartaric acid exist?

    6. Build a model of butane. Rotate the bond between C-2 and C-3 and identify anti, gauche and the two eclipsed conformations! 7. Build models of cis-1,3-dimethylcyclohexane and trans-1,3-dimethylcyclohexane.

    One of the two isomers is more stable than the other. Which? Why? Study the conformations by turning one chair conformation into the other and looking at the axial and equatorial bonds. Draw plane formulae, stereo formulae and Newman projections!

  • KAROLINSKA INSTITUTET Department of Medical Biochemistry & Biophysics Biomedical program (Candidate): General and organic chemistry SEMINAR 6 Thermodynamics & kinetics 1. For a reaction at standard conditions, calculate: a) S, if H = 65.1 kJ/mol and G = 68.7 kJ/mol b) G, if H = -37.3 kJ/mol and S = -146.6 J/(mol*K) c) H, if S = 156.4 J/(mol*K) and Keq = 0.668 2. During aerobic metabolism in living cells (cell respiration), glucose is broken down to release

    energy that then can be used to drive many energy-requiring processes. The energy currency is called ATP, adenosintriphosphate. In the cell 38 ATP-molecules are formed per degraded glucose molecule. Theoretically, what is the maximum number of ATP-molecules that could be formed? How many percent of the energy of a glucose molecule are effectively used by the cell (energy efficiency of the cell)? What happens with the rest of the energy?

    ATP + H2O Pi G = -30,5 kJ/mol Glucose + 6O2 6CO2 + 6H2O G = -2840 kJ/mol 3. Calculate, from the free energies for formation (fG), the G for the reaction CH4(g) + 2 O2(g) CO2(g) + 2 H2O(l) fG for H2O = -237,1 kJmol-1 fG for CO2 = -394,4 kJmol-1 fG for CH4 = -50,7 kJmol-1 Is the equilibrium constant K larger or smaller than 1? How is K affected by an increase in pressure? 4. When pure acetic acid (CH3COOH) is poured into water, the two equilibria 1& 2 shown

    below are reached. Assume that the reactions take place at standard conditions.

    a) Calculate H, S and G for reaction 1. Will the water become warmer or colder when the acetic acid is mixed in? Why is it important to poor the acid into the water, and not vice versa (SIV)? What happens with the entropy during reaction 1 and how can it be explained? Is reaction 1 spontaneous? What does that mean for the equilibrium?

    b) Calculate H, S, G and the equlibrium constant for reaction 2. What happens with the entropy in this case and why is that so? What is the concentration of H+ if one dissolves a

  • total of 0.1 mol acetic acid in 1 l water at 25 C, 1 atm? (use the formula for second degree equations or make an approximation). What pH would it correspond to?

    1. CH3COOH(l) CH3COOH(aq) 2. CH3COOH(aq) CH3COO-(aq) + H+(aq) Thermodynamic data:

    fH0 (kJ/mol) S0 (J/(K*mol)) CH3COOH(l) -484,5 159,8 CH3COOH(aq) -485,76 178,7 CH3COO-(aq) -486,01 86,6 H+(aq) 0 0

    5. Based on previous knowledge about water (general education) combined with your knowledge of thermodynamics, what can you say about magnitude and sign of H, S, G and the equilibrium constant for the reaction H2O(l) H2O(g) at 1 atm and temperatures a) 25 C b) 100 C c) 150 C Explain also how G can change sign.

    6. The equilibrated mix

    SO2(g) + NO2(g) SO3(g) + NO(g) contains at 500K 0.30 mol SO3, 0.20 mol NO, 0.05 mol NO2 and 0.40 mol SO2. a) What is the G of the reaction? Is it spontaneous? b) How many mol NO have to be added to increase the amount of NO2 to 0.10 mol?

    Temperature and pressure are constant. 7. a) The rate, kinetics of a reaction is dependent on three factors. Which?

    b) Show with an energy diagram how a catalyst, e.g. an enzyme, can change the kinetics of a reaction without affecting the equilibrium.

    8. Look at the following energy diagram of an enzyme-catalyzed reaction: a) How many steps are involved? b) Which step is most exergonic? c) Which step is the slowest? EnergyReactionprogress