NE 224-Tutorial#1, Starting September 15, 2016

1. The following chemical species are relevant to biochemical molecules. Sketch the species, using lines to
represent bonds and letters to represent atoms or groups.
a. C-based groups:
CH4 methane (related to CH3 methyl group)
CH3-CH3 ethane (related to CH2-CH3 ethyl group)
CH2=CH2 ethylene (double bonds are common in lipids)
C6H6 benzene (appears as C6H5 phenyl group (e.g. in the amino acid phenylalanine)
b. C- & O-based groups:
general alcohol, use R for the general part. Indicate the hydroxyl group
general aldehyde, use R for the general part. Indicate the carbonyl group
general ketone, use R for the general part. Indicate the carbonyl group
general carboxylic acid, use R for the general part
general ester, use Rs for the general part
general ether, use Rs for the general part
c. C- & S- based groups:
general thiol, use R for the general part. Indicate the sulfhydryl group.
thioether, use Rs for the general part (e.g. in the amino acid methionine)
disulfide, use Rs for the general part (these can be formed from the reaction of 2 thiols, we will
see this later as covalent linkages in proteins)
d. C-, N- & O- based groups:
ammonia
primary (1) amine, use R for the general part. Indicate the amino group
secondary (2) amine, use R for the general part (e.g. in amino acids)
primary (1) amide, use R for the general part (e.g. side chain of amino acid asparagine)
secondary (2) amide, use Rs for the general parts (e.g. peptide bond)
tertiary (3) amide, use Rs for the general parts (e.g. in peptide linkage of amino acid proline)
e. C-,P-& O-based groups (draw the ionization state that you would expect to be predominant at neutral pH):
phosphoric acid
phosphate ester, use R for the general part. Indicate the phosphoryl group.
phosphate diester, use R for the general parts (e.g. in DNA, RNA)
2. Draw all possible hydrogen bonds that can be made by the conjugate base from of the common buffer
component, TRIS (tris(hydroxymethyl)aminomethane, and the neutral, zwitterionic form of the amino
acid, asparagine (you may need to look a little ahead in the course content for this).
3. a. How would you use H3PO4 to make phosphate buffer at pH 6.5? Include all the steps; you do not need
to calculate the actual amounts of the chemicals to weigh out, but indicate the relative amount of acid or
base you would need to add to make the buffer.
b. How would you make the buffer from NaH2PO4? From Na2HPO4? From Na3PO4?
c. Using the best method for making buffers discussed in class, explain how you would make 1.0 liter of
50 mM phosphate buffer at pH 6.5. You can look up the molecular weights online at the Sigma-Aldrich
web site.
4. a. Write two thermodynamically favorable reactions, each one using one (1) of the 2 following reactions
and the reaction for the hydrolysis of ATP to ADP (or the reverse reaction). Calculate the Go for each
of the reactions you have written. (Pi is inorganic phosphate, or H2PO4-)
(1)
phosphocreatine + H2O creatine + Pi
-43.1 kJ mol-1
(2)
glucose-6-phosphate + H2O glucose + Pi
-13.8 kJ mol-1
b. Calculate the Keq for each of the reactions you have written.
c. How do the equations you wrote illustrate the concept of energy currency?