KE7001 Biochemistry Lectures

Amino acids and proteins

Reading material: Stryer chapter 3.1-3 (Horton Chapter 3 and 4)

Abstract: We will begin our study of proteins by zooming in on the two proteins used by mammals to transport and store oxygen: hemoglobin and myoglobin.

Proteins are polypeptide chains consisting of from roughly 50 to several thousand amino acid residues. In nature, 20 different amino acids are commonly used to build polypeptide chains. Proteins have unique amino acid sequences that are specified by genes. The amino acid sequence in turn specifies the range of conformations that the protein may adopt.

Water-soluble proteins (e.g. many enzymes) have amino acid sequences that fold into (almost) unique compact globular structures. It is this folded structure, or shape, that gives the protein its functional properties and allows it to work e.g. as an enzyme.

We will look at the structure and properties of individual amino acids and see how amino acids are linked by peptide bonds into polypeptide chains. We will see how polypeptide chains can wrap up and fold into compact globular structures.

Key concepts:
4°, 3°, 2°, 1° structure
Subunit, domain
General amino acid structure
Types of amino acid residues (polar, hydrophobic, charged etc)
The peptide bond
Rigid and polar peptide unit
Polypeptide chains
Primary structure, N-terminus, C-terminus
Main chain
Side chain
Secondary structure: alpha helix, beta strand, turns

Links:
Check out this excellent library of amino acids from the Molecular Models for Biochemistry at CMU site.

Here is a simple, one-page amino acid table summarizing basic information about the amino acids found in proteins.

From the MIT hypertextbook:
Fisher projections of the L-amino acids found in proteins
The peptide bond
From primary to quaternary structure

This on-line quiz from the Deparment of Biochemistry at Stockholm University might help you memorize amino acid structures and names.

Test your knowledge about amino acids by taking this interactive quiz.

To lecture index