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EK-130
Lab 4: Amino Acids. Hydrophobicity. Hydrogen
bonds.
For using some of the webpages during this lab, you need to download and install the
program Chime. Go to the webpage
http://www.mdlchime.com/chime/
Register, download the program, and install it by following the instructions on the above
webpage.
A. An easy tutorial on amino acids is at the webpage
http://info.bio.cmu.edu/Courses/03231/LecF00/Lec04/lec04.html
The webpage includes links to a Review Quiz on amino acid basic concepts, a selfguided tour of the amino acids, to an Amino Acid Identification Quiz with Chime
Images, and an Amino Acid Structure Quiz. Play the quiz.
B. Another easy tutorial is at
http://www.indstate.edu/thcme/mwking/amino-acids.html
C. An excellent webpage to look at amino acid structure and properties is
http://www.mcb.ucdavis.edu/courses/bis102/AAProp.html
We use this webpage in the lecture for demonstrations.
D. Another good summary of amino acid properties, including hydrophobicity and
solvent accessibility:
http://www.imb-jena.de/IMAGE_AA.html#Properties
E. Take a self-quiz of the concepts:
http://stingray.bio.cmu.edu/~web/bc/MCQS01/MCQLec04.html
F. The amazing structural complexity of water:
http://www.sbu.ac.uk/water/
HW 4
1. Characterize the twenty common amino acids by filling in the following table.
Name
Name
Single letter
symbol
Charge
(+.- or 0)
Polar or
Nonpolar
Relative Size
(small to large)
Ala
Asp
Asn
Arg
Cys
Gly
Gln
Glu
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
2. Draw the general amino acid structure, naming all the atoms that are common in all
amino acids.
3. Which, in your opinion, are the most hydrophobic amino acids? Why?
4. List the two smallest amino acids.
5. What is the difference between an amino acid and an amino acid residue?
6. Draw the ionized and nonionized forms of acidic and basic residues and note the
approximate pH range in which these forms exist.
6. In nonionized histidine, the imidazole ring can exist as two tautomers, with the
hydrogen atom on either nitrogen atom. The ring is readily protonated, with a pKa value
near 7 at the second N atom. Show all three forms of the His residue.
8. Amino acids are often classified into either hydrophobic or hydrophilic. This simple
binary division is not very applicable to a number of amino acids. List at least four such
amino acids and explain why for each.
10. How to remove and then to restore a disulfide bond in a protein?
11. Why does the N – C bond have limited rotations in Pro?
12. What is the origin of hydrophobicity?
13. What is a hydrogen bond?
14. What amino acid side chains can form hydrogen bonds?
15. What is the zwitterionic form of an amino acid?
16. How can water have a structure?
17. Proteins are large molecules that contain substantial amount of nonpolar atoms.
Nevertheless, the globular (i.e., not membrane-bound) proteins are usually
soluble in water. Why?
18. What is the main contribution to hydration? Explain the role of water in protein
folding.