3.091SC | Fall 2010 | Undergraduate

Introduction to Solid State Chemistry

Organic Materials

31. Biochemistry: Protein Structure

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Session Overview

Modules Organic Materials
Concepts primary, secondary, and tertiary protein structures; protein synthesis
Keywords zwitterion, protonation, deprotonation, titratable, electrophoresis, isoelectric point (pI), isoelectric focusing (IEF), protein synthesis, macromolecule, condensation reaction, peptide bond, disulfide bond, kilopeptide, primary structure, protein sequence, secondary structure, tertiary structure, alpha helix, beta pleated sheet, residue, substituent, conformation, hydrophobic, hydrophilic
Chemical Substances nylon, polyamides, insulin
Applications DNA analysis with electrophoresis gel, laundry detergent


Before starting this session, you should be familiar with:

Looking Ahead

This session is the second of three sessions on biochemistry, and completes the foundation for the next session’s culminating exploration of the structure of DNA.

Learning Objectives

After completing this session, you should be able to:

  • Sketch the structures of various amino acids as a function of pH.
  • Explain the behavior of the zwitterion.
  • Define and show the significance of the isoelectric point (pI).
  • Understand the basis of primary, secondary, and tertiary structures of proteins.
  • Explain the role of hydrophobic and hydrophilic effects in protein structures.


Book Chapters Topics
[PB-EOC] 17-6 through 17-12 in Chapter 17, “Amino Acids, Peptides, and Proteins.” Peptide and disulfide bonds; overview of protein structure; primary, secondary, tertiary, and quaternary structures; protein denaturation

Lecture Video


Lecture Slides (PDF - 1.8MB)

Lecture Summary

The lecture begins with further discussion about zwitterion behavior (introduced in Session 30), with the titration curve used to depict the relationship between degree of protonation and pH. An interesting application of zwitterion behavior is gel electrophoresis, in which an electrified gel column of varying pH allows a mix of different amino acids to be separated and analyzed.

Most of the lecture is devoted to protein structure. The peptide bond is the means of creating long macromolecule chains out of individual amino acids. These chains become a basis of life, as they encode information in different sequences of amino acids. (As an aside, amino acids can be remembered by their 3-letter “airport code” analogs.)

  • Primary structure is the backbone amino acid sequence order.
  • Secondary structure relates to packing, and comes in three forms: 1) the alpha helix, as the chain coils back on itself to maximize hydrogen bonding between “galleries” around the spiral; and 2) the beta pleated sheet, in which hydrogen bonds are maximized between macromolecules; and 3) random structure.
  • Tertiary structure affects the macromolecule’s conformation: a range of interactions between nearby R-groups cause the backbone chain to fold. Mechanisms include covalent (disulfide) and hydrogen bonds, electrostatic attraction, and hydrophobic and hydrophilic interactions.


Problems (PDF)

Solutions (PDF)

For Further Study

Other OCW and OER Content

Content Provider Level Notes
7.01SC Fundamentals of Biology MIT OpenCourseWare Undergraduate (first-year) See Unit 1: Biochemistry
7.343 Protein Folding, Misfolding and Human Disease MIT OpenCourseWare Undergraduate (elective) Seminar on some biological implications of protein tertiary structure

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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