18. Amino Acids and Proteins

Classify each amino acid as polar, nonpolar, acidic, or basic.

a) Glu

b) Val

c) Pro

d) Lys

e) Gln

f) Arg 

Provide one letter codes for amino acids with neutral hydrophilic R groups that participate in H bonding.

Valine is an amino acid with a nonpolar side chain and serine is one with a polar side chain. Draw the two amino acids.

a. Why is the side chain for valine nonpolar, whereas the side chain for serine is polar?

Which amino acid is hydrophilic (dissolves in aqueous solutions)? Why?

a. isoleucine

b. phenylalanine

c. aspartic acid

Cell membranes are studded with proteins. Some of these proteins, involved in the transport of molecules across the membrane into the cell, span the entire membrane and are called transmembrane proteins. The interior of the cell membrane is hydrophobic and nonpolar, whereas both the extracellular and intracellular fluids are water-based.

a. List three amino acids you would expect to find in the part of a transmembrane protein that lies within the cell membrane.

Four of the most abundant amino acids in proteins are leucine, alanine, glycine, and valine. What do these amino acids have in common? Would you expect these amino acids to be found on the interior or on the exterior of the protein?

 Is phenylalanine hydrophilic or hydrophobic? Explain why.

Which of the following amino acids is most likely to be found on the outside of a soluble protein, and which of them is more likely to be found on the inside? Explain each answer. (Hint: Consider the effect of the amino acid side chain in each case and that the protein is folded up into its globular form.)

a. Valine

List the amino acids with side chains that are capable of hydrogen bonding. Draw an example of two of these amino acids hydrogen bonding to one another. For each one, draw a hydrogen bond to water in a separate sketch. Refer to Section 8.2 for help with drawing hydrogen bonds.

What are some differences between each of the following pairs? (16.1, 16.2, 16.3)

c. polar and nonpolar amino acids

How does the polarity of the R group in leucine compare to the R group in serine?

Draw the structure for each of the following amino acids at physiological pH:

a. lysine

Classify each of the amino acids in problem 16.5 as polar or nonpolar. If polar, indicate if the R group is neutral, acidic, or basic. Indicate if each is hydrophobic or hydrophilic.

Draw the structure for each of the following amino acids and put an asterisk (*) next to any chiral carbon centers in your structure:

b. lysine

Classify each of the amino acids in Problem 10.1 as polar (neutral, acidic, or basic) or nonpolar and as hydrophobic or hydrophilic.

Give the three-letter and one-letter abbreviations and identify the functional group in the side chain for each amino acid in Problem 10.1.

Draw the structure for each of the following amino acids and put an asterisk (*) next to any chiral carbon centers in your structure:

c. methionine

Classify each amino acid in Problem 10.4 as polar (neutral, acidic, or basic) or nonpolar and as hydrophobic or hydrophilic.

Isoleucine has the zwitterion structure shown. Draw the structure and give the net charge of isoleucine that will predominate at the indicated pH values (pI = 6.0).

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b. pH 6.0

Glycine has the zwitterion structure shown. Draw the structure and give the net charge of glycine that will predominate at the indicated pH values (pI = 6.0).

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b. pH 12.0