Hydrophobic Amino Acid Essay

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Problem Set 1-Answer Key

BILD1 Spring 2013

1) Using water as an example, explain what a polar molecule is. Using the stick diagram, label which atoms are positively or negatively polarized.

Water, is a compound, that has a very electronegative (pulls electrons towards itself) atom ,Oxygen, that is covalently bonded to 2 Hydrogen atoms (not very electronegative), As a consequence of these covalent bonds – the shared electrons are pulled toward the Oxygen atom and causes Hydrogen to become positively (+) polarized. Oxygen, having drawn the the shared pair of electrons towards itself, becomes negatively polarized. The symbol - δ+ and δ- is used to depict positively and negatively polarized atoms, respectively.

δ-

O

H

δ+

δ+H
NOTE: Because water is polar – it can H-Bond.
2) For each molecule shown, decide if it can accept a hydrogen bond, donate a hydrogen bond, do both, or do neither. Circle the H that acts as a donor H. Indicate the H’s that can not participate in H bonding with an arrow.
a) Donate and Accept (Oxygen accepts) b) Accept only (Oxygen accepts)

a) CH3- CH20H

c) Donate and Accept (Nitrogen and oxygen

b) CH3-0- CH3
d) No donor, no acceptor

c) CH3- NH-CO-CH3

e) Donate and Accept (Oxygen accepts)

d) CH3- CH2- CH2- CH3
f) No donor, no acceptor

e) CH3- CH0H-CHOH- CH3

f) H2

= Hydrogen that can not participate in H-Bonds = Donor Hydrogen

3) Look at the molecules listed below. a) Which of the molecules are hydrophobic? b) Which are hydrophilic? c) Which are amphipathic? d) Which molecules can ionize? e) Write each of the molecules in molecular short hand (I will give you one (D)).

A) B) C) D) E)

E is hydrophobic A, B, and C are hydrophilic D is amphipathic B, C, and D can ionize (Note- this exercise is to help familiarize yourself with how organic molecules are written in shorthand – key is to identify functional grounds that makes molecules, hydrophobic, hydrophiic, polar, nonpolar, can ionized, etc.)

4) HCl is a strong acid. What distinguishes a strong acid from a weak one? Describe the pH scale. What would be the pH of a 0.1 M solution of HCl? What would be the concentration of OH- in this solution?

Strong acids completely dissociate to their ionic form in water (e.g. H+ and Cl- ions). Weak acids partially dissociate, and the binding and release of H+ ions is reversible (Carbonic acids was used as a example in class). pH scale compresses the range of [H=] and [OH-] by employing logarithms – pH

declines as the [H+] increases ([OH-] decreases) and pH increases as [H+] decreases ([OH-] increases) The pH of 0.1 M solution of HCL is 1 [H+] = - log 10-1 M = -(-1) = 1; [OH-] is 10-13 M (10-1 x 10-13 equal 10-14)
5) Each of the molecules below is placed into an aqueous buffered solution (pH ~ 7.0). What would be the net negative charge of each molecule in solution? Indicate the charged functional group with the charge it will have at those conditions (This is not as hard as you think – think about the functional groups!). -1 a) CH3- CH2-CH2-CH2-CH2-COOH b) CH3- CH2-CH2-CH2-CH2-CHO -1 +1 c) NH2-CH2-CH2-CH2-COOH -1 d) CH3-O-HPO2-O- CH2- CH3 -2 +1 e) H2PO4- CH2- CH2- NH2 minus 1 net no net charge no net charge minus 1 net minus 1 net

6) Why is the fatty acid shown below considered an unsaturated fatty acid? Indicate the fatty acid portion of the molecule, and circle the features or features of the molecule that the term “unsaturation” refers to.

This fatty acid is unsaturated because of the presence of double bonds which can actually form kinks and can affect the packing of these fatty acids (e.g. butter – saturated – solid at room temp; vegetable oil has unsaturated fatty acids – and is
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