Introduction to Biochemistry: Amino Acids and Their Properties

Course Logistics and Expectations

  • Instructor: Dr. Daniel J. Slade (dslade@vt.edu)

  • Office: 4115

  • Class Schedule: Monday, Wednesday, Friday from 11:15 AM - 12:05 PM.

  • Teaching Assistant (TA) Sessions: Wednesday evenings from 5:30 PM - 6:20 PM, usually led by Teaching Assistants.

  • Teaching Assistants:

    • Nanqi Liang (Graduate Teaching Assistant)

    • Yale Yeo (Undergraduate Teaching Assistant)

  • Instructor Expectations (from Dr. Slade to students):

    • Create a safe and respectful learning environment for everyone.

    • Be fair with grading.

    • Provide materials necessary for success in this intensive biochemistry course.

    • Be flexible if the teaching format needs to change.

  • Student Expectations (from Dr. Slade to students):

    • Be respectful to fellow students, the professor, and TAs in all interactions (online conversations, print questions, video chat during problem sessions).

    • Class Attendance: Expected, whether online or in person.

      • Missing class: Lectures will be posted on Canvas a couple of hours before class and are also useful for review.

      • Wednesday night sessions (5:30 PM, Engel 223) with the Professor and TA are highly encouraged.

  • Quizzes: Pop quizzes account for 10\% of the total grade.

  • Tests: Held on Wednesday nights at 5:30 PM in Engel 223.

  • Canvas: The primary platform for syllabus, schedule, announcements, modules, quizzes, assignments, discussions, and grades.

Grading and Evaluation

  • Quizzes: 7 quizzes in total; the top 6 scores will be counted.

  • Final Exam Policy: If a student scores better on the Final Exam than on one of their tests, the final exam score will be averaged with the lower test score to replace it and give a better grade.

Amino Acids: Introduction and Structure

  • Topic: Amino Acids and the Peptide Bond (Chapter 4).

  • Section 4.1: What are the structures and properties of amino acids?

  • Section 4.1a: Typical amino acids contain a central tetrahedral carbon atom.

  • Anatomy of an Amino Acid (at neutral pH) - Figure 4.1:

    • Central Atom: Alpha-Carbon (C_ ext{\alpha}), which is a tetrahedral carbon atom.

    • Attached Groups:

      • Amino group (NH_3^+)

      • Carboxyl group (COO^-)

      • Hydrogen atom (H)

      • Side chain (R group) - This determines the specific properties of the amino acid.

    • Zwitterion: Amino acids exist predominantly in this dipolar form at neutral pH, meaning they have both a positive charge (on the amino group) and a negative charge (on the carboxyl group).

The 20 Common Amino Acids of Proteins

  • Amino acids are categorized based on their side chain properties:

    • Nonpolar Side Chains: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Methionine (M), Phenylalanine (F), Tryptophan (W), Proline (P).

    • Polar Side Chains: Serine (S), Threonine (T), Cysteine (C), Tyrosine (Y), Asparagine (N), Glutamine (Q).

    • Electrically Charged Side Chains:

      • Acidic: Aspartate (D), Glutamate (E).

      • Basic: Lysine (K), Arginine (R), Histidine (H).

  • Critical Detail: Proper charge labeling (e.g., NH_3^+ for protonated amino group, COO^- for deprotonated carboxyl group) is essential when drawing amino acids.

Tips for Drawing Amino Acids and Polypeptide Chains

  • Resource: Great overview found at Harvard's online LabXchange.

  • Example: Drawing a peptide with the sequence NH_3^+-WRM-COO^-, as it would predominantly exist at physiological pH.

    1. Draw the Peptide Backbone: Consists of nitrogen-carbon-carbon for each amino acid. Repeat this pattern for the number of amino acids in the peptide (3 times for WRM).

      • Backbone nitrogen atoms (except for proline) always have one hydrogen atom.

    2. Draw the C-terminus and Backbone Carbonyl Groups:

      • The N-terminal free amino group must be bound to an alpha carbon, which is itself bound to a carbonyl carbon. This pattern continues until the C-terminus.

      • The C-terminus (COO^-) and carbonyl groups (C=O) for each residue are added.

    3. Draw the Side Chains: Add the specific R-groups for Tryptophan (W), Arginine (R), and Methionine (M) to their respective alpha carbons.

    4. Check for Ionizable Groups: Ensure each group is drawn with the correct protonation state matching the specified pH (e.g., physiological pH).

      • The peptide bond itself does NOT ionize.

      • N-terminus: pK \approx 9.6; if pK > pH, it's protonated (H_3N^+).

      • C-terminus: pK \approx 2.5; if pK < pH, it's deprotonated (COO^-).

      • Side chain of Arginine: pK \approx 12.5; if pK > pH, it's protonated (=NH_2^+).

    5. Check for Common Mistakes:

      • Incorrect amino acid at the N-terminus.

      • Failure to ionize the N- and C-termini correctly.

      • Incorrectly drawn side chains (e.g., rings, miscounting carbons, omitting the linking carbon for rings).

Unnatural Amino Acids (UAA)

  • Concept: Incorporating new chemistry into proteins by using amino acids beyond the standard 20 canonical ones.

  • Examples of UAAs: Illustrated structures include variations with hydroxyl groups, iron, sulfur, mercury, and other novel functionalities.

  • How to Incorporate UAAs: Achieved by re-engineering the protein synthesis machinery.

Mechanism of UAA Incorporation

  1. Orthogonal Synthetase: An engineered aminoacyl-tRNA synthetase that specifically recognizes the unnatural amino acid (UAA) and an orthogonal tRNA.

  2. Orthogonal tRNA: An engineered tRNA that is not recognized by any endogenous synthetase and recognizes a unique codon in the mRNA.

    • The orthogonal synthetase charges the orthogonal tRNA with the unnatural amino acid, using ATP (Adenosine Triphosphate) to form AMP (Adenosine Monophosphate) and PPi (Pyrophosphate).

    • Ligase: An enzyme that catalyzes the linking together of two molecules, often using ATP.

  3. Unique Codon: A stop codon (or other rarely used codon) in the mRNA is reprogrammed to specify the unnatural amino acid.

  4. Ribosome: Translates the mRNA, and when it encounters the unique codon, the orthogonal tRNA carrying the UAA inserts the unnatural amino acid into the growing protein chain.

  5. Result: A protein containing the unnatural amino acid at a specific site.

Amino Acids Outside the 20 Canonical

Selenocysteine (SeC)

  • Comparison: Similar to Cysteine (C), but with Selenium (Mw = 78.96) replacing Sulfur (Mw = 32.06).

  • Prevalence:

    • More than 100 types of selenocysteine-containing proteins have been characterized.

    • Roughly half of eukaryotes (especially higher plants) and three-fourths of all bacteria do not contain selenoproteins.

  • Uniqueness: Selenocysteine is the only common amino acid that humans can synthesize, but higher plants cannot.

  • Significance: Its unique and powerful properties will be covered in Lecture 2.

  • Incorporation: Selenocysteine can be incorporated into proteins using specific engineered systems, sometimes involving Cys-auxotrophic strains.

Selenomethionine

  • Use in Research: Selenium (Mw = 78.96) is considered a heavy atom.

  • Application: Proteins containing selenomethionine (instead of methionine) can be used in X-ray crystallography to solve their three-dimensional structures due to the anomalous scattering properties of selenium.

Auxotrophy

  • Definition: (from Ancient Greek: "nourishment") The inability of an organism to synthesize a particular organic compound required for its growth.

Upcoming Lecture

  • Lecture 2 (Wednesday, August 27th): Will cover the acid-base properties of amino acids, including how amino acids are weak polyprotic acids (Section 4.2a).