3: Amino Acids
Students identify amino acids by their side chains, classify R-groups by polarity and charge, predict amino acid protonation states at given pH values, and analyze peptide bond formation.
LibreTexts reference: Unit 1, Chapter 3: Amino Acids and Peptides 
Matching Amino Acids to Properties (Long Tables)
Click to show Matching Amino Acids to Properties (Long Tables) example problem
Match each of the following amino acids with their corresponding descriptions.
Note: Each choice will be used exactly once.
| Your Choice | Prompt | |
|---|---|---|
| 1. histidine | ||
| 2. glutamate | ||
| 3. threonine | ||
| 4. alanine | ||
| 5. methionine |
Drag one of the choices below:
- A. a non-polar amino acid with a side chain containing a sulfur atom that is NOT available for chemical reactions
- B. a polar amino acid that is a methylated form of serine
- C. a negatively charged amino acid with a large, carboxylate (-COOH) side chain
- D. an aromatic amino acid with a side chain containing a 5-membered nitrogenous ring and a pKa close to pH 7
- E. a non-polar amino acid, with a single methyl group (-CH3) as its side chain
Matching Amino Acids to Descriptive Properties
Click to show Matching Amino Acids to Descriptive Properties example problem
Match each of the following amino acids with their corresponding descriptions.
Note: Each choice will be used exactly once.
| Your Choice | Prompt | |
|---|---|---|
| 1. serine | ||
| 2. glutamate | ||
| 3. asparagine | ||
| 4. aspartate | ||
| 5. histidine |
Drag one of the choices below:
- A. an aromatic amino acid with a side chain containing a 5-membered nitrogenous ring and a pKa close to pH 7
- B. a negatively charged amino acid with a small, carboxylate (-COOH) side chain
- C. a polar amino acid with a shorter amine-substituted carboxylate (amide) -C(=O)NH2 group
- D. a negatively charged amino acid with a large, carboxylate (-COOH) side chain
- E. a polar amino acid with the smallest polar side chain
Amino Acids from Properties (Long Tables)
Click to show Amino Acids from Properties (Long Tables) example problem
Which one of the following amino acids correspond to the description 'a positively charged amino acid with a long, flexible side chain containing 3 nitrogen atoms (guanidinium)'.
Amino Acids from Descriptions
Click to show Amino Acids from Descriptions example problem
Which one of the following amino acids correspond to the description 'a polar amino acid that is capable of thiol (-SH) chemistry'.
Alanine Charge States at Different pH Values
Click to show Alanine Charge States at Different pH Values example problem
Alanine Charge States
Alanine has two pKa values: 2.34 and 9.69.
Question: Which one of the following is the correct charge state of alanine at pH 10.1?
Select one answer.
Alpha Amino Acids
Click to show Alpha Amino Acids example problem
Which of the following (I, II, III, IV) is an α-amino acid?
Select one answer.
Histidine Protonation States at Specific pH Values
Click to show Histidine Protonation States at Specific pH Values example problem
Histidine Protonation States
Histidine has three pKa values: 1.82, 6.00, and 9.17.
Question: Which one of the following is the correct protonation state of histidine at pH 6.6?
Select one answer.
Ionic Bond Formation in Amino Acid Side Chains
Click to show Ionic Bond Formation in Amino Acid Side Chains example problem
Based on the chemical properties of amino acid side chains, which pair of amino acids listed below can form an ionic bond between their side chains?
Amino Acid Names from Chemical Structures (4 Choices)
Click to show Amino Acid Names from Chemical Structures (4 Choices) example problem
Match the amino acid structures to their names.
Note: Each choice will be used exactly once.
| Your Choice | Prompt | |
|---|---|---|
| 1. | ||
| 2. | ||
| 3. | ||
| 4. |
Drag one of the choices below:
- A. asparagine
- B. aspartic acid
- C. glutamic acid
- D. serine
Dipeptide Sequences from Structures
Click to show Dipeptide Sequences from Structures example problem
peptide_4d88
A dipeptide is made up of two (2) amino acids. The figure above shows one such dipeptide with an unknown sequence. Your task is to find out the two (2) letter sequence of this dipeptide.
Here is a step-by-step guide to help you:
- Consult an amino acid guide for reference. You can find a PDF guide on Blackboard under "Exam and Quiz" in the "Old Exams" section, with the filename bchm_exam-help_sheet.pdf, or search online for a visual guide that shows all 20 amino acids with their single-letter codes.
- Identify the amino-terminal end, represented as NH3+ and highlighted in bright green. Distinguish between the general nitrogens in amino acid backbones (denoted as NH) and the nitrogen in amino acid side chains.
- The one (1) peptide bonds connecting the two (2) amino acids is/are highlighted in bright green, making it easier to distinguish the two (2) amino acids.
- Examine the side chain for each of the two (2) amino acids to determine their single-letter amino acid code.
- Once you have identified the single-letter codes for the two (2) side chains, list them in the amino to carboxyl (N→C) direction. This is the standard method for writing peptide sequences.
- You answer will consist only two (2) letters, no spaces and no other punctuation.
Dipeptide Sequences from Descriptions
Click to show Dipeptide Sequences from Descriptions example problem
peptide_1138
A dipeptide is made up of two (2) amino acids. The figure above shows one such dipeptide with an unknown sequence. Your task is to find out the two (2) letter sequence of this dipeptide.
Here is a step-by-step guide to help you answer the question:
- Consult an amino acid guide for reference. You can find a PDF guide on Blackboard under "Exam and Quiz" in the "Old Exams" section, with the filename bchm_exam-help_sheet.pdf, or search online for a visual guide that shows all 20 amino acids with their single-letter codes.
- Identify the amino-terminal end, represented as NH3+ and highlighted in bright green. Distinguish between the general nitrogens in amino acid backbones (denoted as NH) and the nitrogen in amino acid side chains.
- The one (1) peptide bonds connecting the two (2) amino acids are highlighted in bright green, making it easier to distinguish the two (2) amino acids.
- Examine the side chain for each of the two (2) amino acids to determine their single-letter amino acid code.
- List the single-letter amino acid codes in the amino to carboxyl (N→C) direction. This is the standard method for writing peptide sequences.
Select the correct peptide sequence from the options below:
Tripeptide Sequences from Structural Descriptions
Click to show Tripeptide Sequences from Structural Descriptions example problem
peptide_ecf9
A tripeptide is made up of three (3) amino acids. The figure above shows one such tripeptide with an unknown sequence. Your task is to find out the three (3) letter sequence of this tripeptide.
Here is a step-by-step guide to help you answer the question:
- Consult an amino acid guide for reference. You can find a PDF guide on Blackboard under "Exam and Quiz" in the "Old Exams" section, with the filename bchm_exam-help_sheet.pdf, or search online for a visual guide that shows all 20 amino acids with their single-letter codes.
- Identify the amino-terminal end, represented as NH3+ and highlighted in bright green. Distinguish between the general nitrogens in amino acid backbones (denoted as NH) and the nitrogen in amino acid side chains.
- The two (2) peptide bonds connecting the three (3) amino acids are highlighted in bright green, making it easier to distinguish the three (3) amino acids.
- Examine the side chain for each of the three (3) amino acids to determine their single-letter amino acid code.
- List the single-letter amino acid codes in the amino to carboxyl (N→C) direction. This is the standard method for writing peptide sequences.
Select the correct peptide sequence from the options below:
Peptide Sequences with Four Amino Acids
Click to show Peptide Sequences with Four Amino Acids example problem
peptide_d99d
A tetrapeptide is made up of four (4) amino acids. The figure above shows one such tetrapeptide with an unknown sequence. Your task is to find out the four (4) letter sequence of this tetrapeptide.
Here is a step-by-step guide to help you answer the question:
- Consult an amino acid guide for reference. You can find a PDF guide on Blackboard under "Exam and Quiz" in the "Old Exams" section, with the filename bchm_exam-help_sheet.pdf, or search online for a visual guide that shows all 20 amino acids with their single-letter codes.
- Identify the amino-terminal end, represented as NH3+ and highlighted in bright green. Distinguish between the general nitrogens in amino acid backbones (denoted as NH) and the nitrogen in amino acid side chains.
- The three (3) peptide bonds connecting the four (4) amino acids are highlighted in bright green, making it easier to distinguish the four (4) amino acids.
- Examine the side chain for each of the four (4) amino acids to determine their single-letter amino acid code.
- List the single-letter amino acid codes in the amino to carboxyl (N→C) direction. This is the standard method for writing peptide sequences.
Select the correct peptide sequence from the options below:
Tetrapeptide Net Charge from pKa Values (5 Choices)
Click to show Tetrapeptide Net Charge from pKa Values (5 Choices) example problem
tetrapeptide_5f5d
The tetrapeptide above is shown in its fully neutral (uncharged) drawing form. Using the approximate pKa values below, estimate the net charge of this peptide at pH 2.2.
Sequence (N to C): Ser-Leu-Lys-Asp
Approximate pKa values for the groups in this peptide:
- alpha-amino group (N-terminus): 9.0
- alpha-carboxyl group (C-terminus): 2.0
- Lys side chain: 10.5
- Asp side chain: 3.7
Select the net charge at pH 2.2:
Amino Acids from Chemical Structures
Click to show Amino Acids from Chemical Structures example problem
Which amino acid is represented by the chemical structure shown above?
Amino Acids from Chemical Structures (7 Choices)
Click to show Amino Acids from Chemical Structures (7 Choices) example problem
Which amino acid is represented by the chemical structure shown above?
Peptide Sequences (Fill in the Blank)
Click to show Peptide Sequences (Fill in the Blank) example problem
peptide_865a
A pentapeptide is made up of 5 amino acids. The figure above shows one such peptide chain with an unknown sequence. Your task is to find out the sequence of this pentapeptide.
Here is a step-by-step guide to help you:
- Looking at an amino acid guide can help. There is a PDF guide on Blackboard under "Exam and Quiz" with the "Old Exams" and the filename bchm_exam-help_sheet.pdf. You can also search online to find a visual grid that shows all 20 amino acids with their single-letter codes.
- First, identify the amino-terminal end, which is represented as NH3+ and highlighted in bright green. It's important to differentiate between the general nitrogens found in amino acid backbones (denoted as NH) and the nitrogen in the side chains of amino acids. Among amino acids, only lysine has a side chain with three hydrogens, resembling the NH3+ of the amino-terminal end.
- The peptide bonds are highlighted in bright green, helping you see the different amino acids.
- Look at the side chains of each amino acid to figure out their single-letter amino acid code.
- Once you know the single-letter codes for the 5 side chains, list them in the amino to carboxyl (N→C) direction. This is the accepted way to write peptide sequences.
- The correct sequence of letters will be a five-letter English word. This word is also an answer in the New York Times Wordle™ game.