3.091SC | Fall 2010 | Undergraduate

Introduction to Solid State Chemistry

Organic Materials

30. Biochemistry: Amino Acids

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Session Overview

Modules Organic Materials
Concepts amino acids, peptides, proteins
Keywords molecular biology, biomolecule, amino acid, polymer, protein, pH, Brønsted base, amine group, carboxylic acid, alpha carbon, substituent, hydrophilic, chirality, enantiomer, optical activity, polarized light, dextrorotatory, levorotatory, sugars, invert sugar, racemic, teratogenic, zwitterions, Henderson-Hasselbalch equation, protonation, Le Châtelier principle
Chemical Substances thalidomide, Ritalin, trinitrotoluene (TNT)
Applications biology, pharmaceuticals, explosives


Before starting this session, you should be familiar with:

Looking Ahead

This is the first of three sessions on biochemistry.

Learning Objectives

After completing this session, you should be able to:

  • Understand the common characteristics of amino acids.
  • Highlight the variations among individual amino acids.
  • Describe the role of chirality in amino acid chemistry.
  • Predict the influence of pH on amino acid chemical structure and properties.


Book Chapters Topics
[Saylor] 12.8, “Polymeric Solids.” Introduction to biological polymers (peptides and proteins)
[Saylor] 24.6, “The Molecules of Life.” Survey of proteins, carbohydrates, lipids, and nucleic acids
[PB-EOC] 17-1 through 17-4 in Chapter 17, “Amino Acids, Peptides, and Proteins.” Overview and configurations of the 20 common amino acids; acid-base properties; isoelectric point pI
[RH] 3, “Amino Acids and the Primary Structures of Proteins.” General structure of amino acids; details on each of the 20 common amino acids; other amino acids and derivatives; ionization of amino acids; creating proteins with peptide bond links

Lecture Video


Lecture Slides (PDF - 1.2MB)

Lecture Summary

Biochemistry is an integrative topic that connects many prior topics, and governed by the same laws that apply to inanimate matter. Biology – especially at the molecular level - is solid state chemistry. “Mother Nature is a polymer engineer gone wild!”

This lecture starts with amino acids as the building blocks of proteins, and in particular looks at their structure.

  • All amino acids have an sp3 hybridized carbon at their center (aka “alpha carbon”).
  • Three of the four bonds are identical in all amino acids (amine group, lone hydrogen, carboxyl group). The fourth bond is the side chain — “R” or the substituent, i.e. “nature’s choice.”
  • Twenty amino acids comprise all proteins.
  • Nineteen of these twenty amino acids in proteins are chiral.

Prof. Sadoway surveys some amino acid properties, focusing on behavior in water. In an aqueous solution, the amino acid transfers a proton, becoming a zwitterion. Applying the Le Châtelier principle to scenarios of increased and decreased pH, Prof. Sadoway walks through the amino acid chemical responses, concluding: “This is what animates the stuff of life!”

Chirality can have profound implications for the biological response to particular chemicals. The drug thalidomide contained an enantiomer that had unforseen interactions with a human enzyme, leading to a wave of birth defects.

The lecture ends with discussion of the kinetics of organic compounds, specifically the extreme case of explosives. Prof. Sadoway describes the tremendous damage caused by the 1917 Halifax explosion, in which a ship loaded with TNT and other explosive chemicals caught fire in the harbor, causing the largest explosion of the pre-nuclear age.


Problems (PDF)

Solutions (PDF)

Textbook Problems

[saylor] Sections Conceptual Numerical
[Saylor] 12.8, “Polymeric Solids.” 1 none

For Further Study

Supplemental Readings

Halifax Explosion



Michael Jackson. “Man in the Mirror.” Bad. Epic Records, 1987.

Other OCW and OER Content

Content Provider Level Notes
7.01SC Fundamentals of Biology MIT OpenCourseWare Undergraduate (first-year) See Unit 1: Biochemistry

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Course Info

As Taught In
Fall 2010
Learning Resource Types
Course Introduction
Exams with Solutions
Lecture Notes
Lecture Videos
Problem Sets with Solutions
Recitation Videos
Problem Sets
Exam Materials