Draw the structure of the following amino acids, dipeptides, and tripeptides at low pH (pH 1) and high pH (pH 14). At each pH, assume that all functional groups that might do so are ionized.

e. Gln-Ala-Asn

Interactions of amino acids on the interior of proteins are key to the shapes of proteins. In group (a), which pairs of amino acids form hydrophobic interactions? In group (b), which pairs form ionic interactions? Which pairs in group (c) form hydrogen bonds?

a. 1 Pro . . . Phe

   2 Lys . . . Ser

   3 Thr . . . Leu

   4 Ala . . . Gly

Draw the hexapeptide Asp-Gly-Phe-Leu-Glu-Ala in linear form showing all of the atoms, and show (using dotted lines) the hydrogen bonding that stabilizes this structure if it is part of an α-helix.

Compare and contrast the characteristics of fibrous and globular proteins. Consider biological function, water solubility, amino acid composition, secondary structure, and tertiary structure. Give examples of three fibrous and three globular proteins. (Hint: Make a table.)

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.

Threonine has two chiral centers. Draw L-threonine and indicate which carbon atoms are chiral. Which carbon atom is responsible for D and L configuration?

Name four biological functions of proteins in the human body, and give an example of a protein for each function.

What kind of biological function would each of the following proteins perform?

a. Human growth hormone

What kind of biological function would each of the following proteins perform?

c. Protease

What amino acids do the following abbreviations stand for? Draw the structure of each.

a. Val

Name and draw the structures of the amino acids that fit the following descriptions:

a. Contains a thiol group

Name and draw the structures of the amino acids that fit the following descriptions:

a. Contains an isopropyl group

Draw leucine and identify any chiral carbon atoms with arrows.

 Is phenylalanine hydrophilic or hydrophobic? Explain why.

At neutral pH, which of the following amino acids has a net positive charge, which has a net negative charge, and which is neutral? (Hint: Draw the various charged forms of each amino acid before deciding.)

a. Asparagine

b. Lysine

c. Proline

Which of the following forms of aspartic acid would you expect to predominate at low pH, neutral pH, and high pH?

a.

b.

c.

Which form of aspartic acid in Problem 18.54 is the zwitterion? What is the pI for the zwitterion?

a.

b.

c.

Proteins are usually least soluble in water at their isoelectric points. Explain.

How could you make the zwitterion of aspartic acid more soluble in water?

Use the three-letter abbreviations to name all tripeptides that contain valine, methionine, and leucine.

Write structural formulas for the two dipeptides that contain leucine and aspartate.

The endorphins are a group of naturally occurring neurotransmitters that act in a manner similar to morphine to control pain. Research has shown that the biologically active parts of the endorphin molecules are simple pentapeptides called enkephalins. Draw the structure of the methionine enkephalin with the sequence Tyr-Gly-Gly-Phe-Met. Identify the N-terminal and C-terminal amino acids.

Identify the amino acids present in the peptide shown and name the peptide using the three-letter abbreviations.

Identify the N-terminal and C-terminal amino acids of the peptide.

What is the sequence of atoms along the "backbone" of a protein?

Bradykinin, a peptide that helps to regulate blood pressure, has the primary structure Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg.

a. Draw the complete structural formula of bradykinin.

Bradykinin, a peptide that helps to regulate blood pressure, has the primary structure Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg.

b. Bradykinin has a very kinked secondary structure. Why?

Give an example of a protein containing primarily alpha-helices. Is this a fibrous or globular protein?

What kind of bond would you expect between the side chains of the following amino acids?

b. Alanine and leucine

What kind of bond would you expect between the side chains of the following amino acids?

c. Aspartic acid and asparagine