14.E: Exercises
- Page ID
- 465681
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Multiple Choice
1. Which of the following is a nonpolar (hydrophobic) amino acid?
a) tyrosine
b) serine
c) valine
d) lysine
2. Which of the following elements is not found in amino acids?
a) hydrogen
b) phosphorus
c) oxygen
d) nitrogen
3. Which one of the following statements about amino acids is true?
a) Twenty-four different amino acids are commonly found in proteins
b) All amino acids contain a carboxylic acid group
c) Amino acids with hydrophobic side chains are insoluble in water
d) Amino acids are linked via a “backbone” of sugar-phosphate bonds
4. Which of the following statements is not true of the amino acids?
a) Some amino acids are obtained only from foods we eat.
b) The R group of amino acids differs from one amino acid to another.
c) Amino acids have an N-terminus, C-terminus, and R groups.
d) All amino acids exist in two stereoisomeric forms.
5. The chemical nature of each amino acid is determined by which of the following groups?
a) amino
b) carboxyl
c) hydroxyl
d) R group (side chain)
6. An amino acid is made up of:
a) alpha carbon linked to hydrogen, hydroxyl group, amino group, and a side chain
b) alpha carbon linked to hydrogen, amino group and carboxylic acid group
c) alpha carbon linked to hydrogen, amino group, carboxylic acid group, and a side chain
d) alpha carbon linked to hydrogen, hydroxyl group, amino group, and a carboxylic acid group
7. Which group of three amino acid side chains can form hydrogen bonds with one another?
a) serine, aspartic acid, threonine
b) phenylalanine, isoleucine, glycine
c) aspartic acid, valine, threonine
d) alanine, tryptophan, histidine
8. Which amino acids would you most expect to find inside a protein’s 3-D structure, away from water?
a) serine, glutamic acid, tyrosine
b) phenylalanine, isoleucine, glycine
c) aspartic acid, valine, threonine
d) alanine, tryptophan, histidine
9. Can glycine form hydrogen bonds with other amino acids?
a) Yes, because it forms random coils between strands of beta sheets.
b) No, because it is nonpolar.
c) Yes, because it is contains an alpha carbon.
d) Yes, because it contains a C=O bond and an N-H bond.
10. What is the side chain (R group) on glycine?
a) -C=O
b) -N-H
c) -CH2-CH3
d) -H
11. The primary structure of a protein
a) is the order of amino acids from one end of the protein to another.
b) is important both genetically and structurally.
c) is the linear sequence of amino acids that are linked together by peptide bonds.
d) all of the above
12. Do all polypeptides have tertiary structure?
a) Yes, because they all have secondary structures that are arranged in 3D space.
b) No, because only proteins have tertiary structure.
c) Yes, because they fold into three types of shapes.
d) No, because polypeptides are smaller parts of protein complexes.
13. Hydrogen bonding is most important in stabilizing the ________ structure of many proteins.
a) primary
b) secondary
c) tertiary
d) quaternary
14. Phosphodiester bonds and peptide bonds share an important feature. What is it?
a) Both are created by dehydration reactions
b) Both are found in proteins
c) Both are used to store high-energy electrons
d) Both are formed by the same enzymes
Warm-Up Questions
1-6. Decide which amino acids best fit the following descriptions:
1. ______ has a nonpolar sidechain and interacts with other aromatic rings.
2. ______ is small, and it does not contain sulfur. It can form hydrogen bonds.
3. ______ The lone electron pair at one of the ring nitrogens makes it important in stabilizing the iron atoms in myoglobin.
4. ______ has an extended basic sidechain.
5. ______ is a bulky, hydrophobic amino acid with a double ring structure
6. ______ is the first amino acid in a primary sequence
7. The image below shows a ball-and-stick model of the dipeptide made of alanine and serine. You can access an interactive model of the molecule here. Indicate the location of the amino-terminus, the carboxyl-terminus, the peptide bond and the R groups on alanine and serine.
https://pubchem.ncbi.nlm.nih.gov/compound/Ala-Ser
8. The image below shows a 2-D structural model of the tripeptide Leu-Leu-His. Indicate the location of the amino-terminus, the carboxyl-terminus, the peptide bond and the three R groups.
Intermediate Questions
1. Explain the chemical features that make proline distinct from other amino acids.
2. Explain why glycine is classified as a non-polar amino acid in proteins.
3. Draw a dipeptide consisting of a polar amino acid at the amino terminus and a non-polar amino acid at the carboxyl terminus.
4. Draw the dipeptide consisting of the amino acid with the shortest R group (other than glycine) at the amino terminus and the amino acid with the largest R group at the carboxyl terminus.
5. What is the net charge on a peptide with the sequence N-Met-Ser-Arg-Gly-Gly-Glu-Ala-Val-Lys-C at physiological pH?
6. What is the net charge on a peptide with the sequence N-Ser-Gly-Tyr-Ile-His-Arg-C at physiological pH?
7. This image shows a “ribbon” structure of the protein phospholipase A2, an enzyme that breaks apart phospholipids. You can access an interactive 3D model of the protein here. Comment on the overall structure of the protein and indicate examples of secondary structure.
https://doi.org/10.2210/pdb1CJY/pdb
8. The image below shows a portion of the protein nucleocapsid, which is encoded by the genome for SARS-CoV-2 (the virus that causes COVID-19). Nucleocapsid binds to viral RNA and packages it into new virus particles inside infected host cells. The image shows the protein alone on the left side, and protein bound to RNA on the right side. RNA is in yellow, the peptide backbone is in magenta, and select amino acid side chains are in purple and turquoise. Identify the amino acids and explain why their structure helps with RNA binding.
Challenge Questions
1. The image below depicts a cross-section of a cell membrane in which a channel protein called aquaporin is embedded. Describe the structural features of the protein. What amino acids are likely to be on the protein exterior, or inside the water channel?
2. Describe the types of bonds/interactions that hold together or stabilize the primary, secondary, tertiary, and quaternary structures of proteins.
Health-Related Questions
1. Changes in temperature and pH, such as found in febrile state or during digestion in the gut, can inactivate proteins by causing them to unfold or misfold. Explain the chemical basis of protein unfolding.
2. Albumin is the most abundant protein in blood serum (approximately 4.0 g/dl) and is an indicator of overall health. Albumin plays an important role as a carrier of fatty acids in the bloodstream. It can also bind to drug molecules and facilitate their transport through the body. Follow the link below to view an interactive 3-D representation of human serum albumin with molecules of stearic acid incorporated into the structure. Use the toolbar at the top of the page to change the way protein and lipid components are displayed. Comment on the secondary and tertiary structure of the protein, the number of stearic acid molecules that are present, and their orientation in the overall structure. Given what you know about lipids, do you think that albumin binding is specific to stearic acid?
https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1E7I&bu=1