1. ATP synthesis
How much energy is stored in bringing together a phosphate and ADP moiety from
infinite separation to bonding distance in solution?
Assume the contribution from the chemical reaction is negligible and water has a
dielectric of 80. Furthermore, we assume the charges are centered on the phosphor
atoms. The phosphor to phosphor distance is 0.26 nm.
2. Proton-motive force
How much energy is required to move one proton from one side to the other side of a
membrane of about 5 nm thickness, given that there is a potential difference of 50 mV
over the membrane?
Is this enough to create one ATP molecule? If not, how much protons have to be
pumped over the membrane in order to build one ATP molecule?
3. Photosynthesis
How many photons need to be absorbed by the bacterial reaction center in
Rhodobacter Sphaeroides in order to create an ATP molecule? The reaction center has
an absorption maximum at 800 nm. What is the efficiency of the photosynthesis
process?
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4. NMR spectroscopy
In the figure is shown a one-dimensional H-NMR spectrum of ethanol (CH3-CH2OH). The peak at 0 ppm is the TMS reference peak.
Type of Proton
Cyclopropane
Primary
Secondary
Tertiary
Vinylic
Acetylenic
Aromatic
Benzylic
Allylic
Fluorides
Chlorides
Bromides
Iodides
Alcohols
Ethers
Esters
Esters
Acids
Carbonyl
Compounds
Aldehydic
Hydroxylic
Phenolic
Enolic
Carboxylic
Amino
Structure
C3H6
R-CH3
R2-CH2
R3-C-H
C=C-H
triple bond,CC-H
Ar-H
Ar-C-H
C=C-CH3
H-C-F
H-C-Cl
H-C-Br
H-C-I
H-C-OH
H-C-OR
RCOO-C-H
H-C-COOR
H-C-COOH
Chemical Shift, ppm
0.2
0.9
1.3
1.5
4.6-5.9
2-3
6-8.5
2.2-3
1.7
4-4.5
3-4
2.5-4
2-4
3.4-4
3.3-4
3.7-4.1
2-2.2
2-2.6
H-C-C=O
2-2.7
R-(H-)C=O
R-C-OH
Ar-OH
C=C-OH
RCOOH
RNH2
9-10
1-5.5
4-12
15-17
10.5-12
1-5
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Use the table to assign the peaks to specific protons.
Predict the spectra of the following organic molecules:
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Methane (CH4) (supposing we can solve this..)
Ethane (CH3-CH3)
Propanol (CH3-CH2-CH2-OH)
Isopropanol ((CH3)2-CHOH)
Pentane (CH3-(CH2)-CH3)
Glycine (NH2-CH2-COOH)
5. Protein NMR
A two-dimensional 1H-15N correlation spectrum has been obtained by transferring
magnetization from amide proton to amide nitrogen to improve signal-to-noise
ratio. Subsequently the frequency of nitrogen (fN) has been collected and thereafter
magnetization has been transferred back to amide proton for monitoring its frequency
(fH). Frequencies are given relative to a reference compound. This type of
measurement is called Heteronuclear Spin Quantum Coherence (HSQC). Below is
shown a typical HSQC spectrum.
What do we learn about the protein structure from this spectrum?
Are there multiple conformations?
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Why is there no proline in the spectrum?
Why does the first residue not give a signal?
Are there any amino acids that give characteristic resonance?
How would the spectrum look like if acquired in the field of twice as strong?
What might the horizontal lines in the spectrum mean?
Why are there very small peaks just above these cross peaks at upper right part of the
spectrum?
6. Projects for next week
Prepare an oral presentation of about 5-10 minutes on one of the following topics:
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Levinthal paradox
Enzymatic mechanism of chemotrypsin, lysozym, or papain
Computer aided drug design
Composition of hair
Hydrophobic effect
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