12 Jun Chemistry 251-601 How many hydrogen bonds can be formed
Question
Chemistry 251-601 – Principles of Biological Chemistry
Problem Set 1
Due on February 10th, 2014
50 points
1. (10 points) (a). How many hydrogen bonds can be formed by the following molecules at
physiological pH? Draw the hydrogen bonding pattern (with the complete structure of amino acids)
that water will form with the side chains of the following amino acids:
1. Lysine
2. Glutamine
3. Serine
(b). How many different pentapeptides are there that contain one residue each of Gly, Asp, Tyr,
Cys, Leu
(c) What is the length of an alpha helix made up of polypeptide chain of 10 residues?
(d). Draw the structure of the dipeptide crosslinked by disulfide bond: Met-Cys and Asp-Cys-Val
2. (5 points) For a reaction A ? B at 298 K, the change in molar enthalpy is -7 kJ.mol-1 and the
change in molar entropy is -25 J. K-1. mol-1). Is the reaction spontaneous? If not, should the
temperature be increased or decreased to make it spontaneous? Explain why. At what
temperature will the reaction be at equilibrium?
3. (5 points) Which of the following amino acids would you expect to find on the inside and which
on the outside of a typical globular protein in solution at neutral pH? Explain your answer.
Glu, Val, Ile, Asn, Ser, Arg, Phe, Met, Lys, Thr.
4. (10 points) Predict the secondary structure of the following polypeptide chain and explain why.
(a). Glu-Ala-Glu-Leu-Lys-Val-Phe
(b). Leu-Val-Val-Tyr-Thr-Cys-Ileu
(c). Gly-Val-Pro-Gly
(d). Gly-Pro-Arg-Gly-Pro-Hyp-Gly-Ser-Ala-Gly
(e). Leu-Val-Ala-Leu-Gln-Lys-Lys-Leu-Lys-Gly-Thr-Glu-Asp-Glu
5. (5 points) The side chain of the amino acid Histidine has a pKa of 6.0. Its ionization can be written
as:
His+ (protonated) ? His (deprotonated) + H+
(a) What is the pH when 20 % of histidine is protonated?
(b) What is the ratio of deprotonated to protonated histidine at pH 6.9?
6. (5 points) For the peptide SADPEPTIDE: (Consider N-terminal and C-terminal pKa to be 9 and 2
respectively, pKa of Asp:3.6, pKa of Glu: 4.2)
(a). What are the charge states of the peptide over the titration curve?
(b). What is the pI of this peptide?
7. (10 points) In answering the following questions, consider dimers of GCN251, a 33 amino acid
parallel coiled coil, the sequence of which is shown below.
GCN251:
H2N-HNNYGQLANPLARIRAEIANLDARGSQMETRGS-CO2H
1NRYMQLA10EVRAIKAE20YLDARVSM30E 33
(a). Given the enthalpy (?HºU = 57.6 kcal•mol-1) and entropy (?SºU = 150 cal.mol-1.K-1) of unfolding of
GCN251, calculate the TM of a [ZT] = 100 ?M solution of GCN251 monomers.
(b). NMR measurements show the N- and C-termini of GCN251 to be non-helical, but the central
region has a 14 amino acid stretch that is helical. Write out the sequence of GCN251, circle the
coiled-coil motif, and write the fourteen amino acids of the coiled coil region into two helical wheel
diagrams. Why did you identify this region as the helical segment?
First 7 amino acids
Second 7 amino acids
Constants
Speed of light in vacuum
Elementary charge
Hartree energy
Permittivity of vacuum
Faraday constant
Plank’s constant
Boltzmann constant
Gravitational constant
Standard acceleration of free fall
Permeability of vacuum
Avagadro’s number
Gas constant
Rydberg constant
c
e
Eh
?0
F
h
kB
G
g
?0
NA
R
R?
2.998×108 m•s-1
1.602×10-19 C
4.359×10-18 J
8.854×10-12 F•m-1
9.649×104 C•mol-1
6.626×10-34 J•s
1.381×10-23 J•K-1
6.672×10-11 N•m2•kg-2
9.807 m•s-1
4?x10-7 H•m-1 (Exact)
6.022×1023 mol-1
8.315 J•K-1•mol-1
Our website has a team of professional writers who can help you write any of your homework. They will write your papers from scratch. We also have a team of editors just to make sure all papers are of HIGH QUALITY & PLAGIARISM FREE. To make an Order you only need to click Ask A Question and we will direct you to our Order Page at WriteDemy. Then fill Our Order Form with all your assignment instructions. Select your deadline and pay for your paper. You will get it few hours before your set deadline.
Fill in all the assignment paper details that are required in the order form with the standard information being the page count, deadline, academic level and type of paper. It is advisable to have this information at hand so that you can quickly fill in the necessary information needed in the form for the essay writer to be immediately assigned to your writing project. Make payment for the custom essay order to enable us to assign a suitable writer to your order. Payments are made through Paypal on a secured billing page. Finally, sit back and relax.
About Writedemy
We are a professional paper writing website. If you have searched a question and bumped into our website just know you are in the right place to get help in your coursework. We offer HIGH QUALITY & PLAGIARISM FREE Papers.
How It Works
To make an Order you only need to click on “Order Now” and we will direct you to our Order Page. Fill Our Order Form with all your assignment instructions. Select your deadline and pay for your paper. You will get it few hours before your set deadline.
Are there Discounts?
All new clients are eligible for 20% off in their first Order. Our payment method is safe and secure.