Amino Acids
Objectives
 Fundamental chemical structure, including stereochemistry, of -amino acids.
 Classification of amino acids.
Why?
Proteins are the “worker bees” for biological systems. They perform functions such as enzymes,
structural, transport, etc. The structure and function of these proteins is determined by their building
blocks, the amino acids. In order to understand these functions we must first understand the structure
and properties of these amino acids. They share some common structural features, but are also
structurally diverse. This activity explores the structural features of amino acids. Just as it is important to
learn terminology and nomenclature, it is important to recognize conventional structural representations.
In addition to the structural representations frequently used in organic chemistry (line-bond, wedgedash, etc.), additional representations are also employed (Fischer projection, etc.). In some structural
representations, a conventional color scheme is used to represent different atoms. One such color
scheme for chemical models is CPK where carbon atoms are black/grey, nitrogen are blue, oxygen are
red, hydrogen are white, and sulfur are yellow.
Pre-class Activity
Model 1. Selected amino acid structures
Each structural formula represents the amino acid in the ionization state that would predominate at pH
7.0 in aqueous solution.
alanine
glutamate
glycine
tyrosine
Key Questions
1. For each of the amino acids in Model 1, either build (with a model kit) or look at (with a
computer – using the “aminoacids.htm” file in the BC327_Tablet_Fall09 folder under Activities
– Structure of Amino Acids) the three-dimensional structure. NOTE: If you copy the entire
“Structure of Amino Acids” folder to your flash drive, you should be able to view the structures
on any computer.
2. In the wedge-dash structure, what does the wedge (
3. In the wedge-dash structure, what does the dash (
) indicate about the bond?
) indicate about the bond?
4. Circle the amine group (neutral or charged) in each amino acid.
5. Place a box around each carboxylic acid group (neutral or charged) in each amino acid?
6. Put a star next to any stereocenter(s) present.
7. List at least three structural aspects common to all the amino acids.
8. Identify at least two structural aspects that are not common to all the amino acids.
9. What is the hybridization of the carbonyl carbon in each amino acid structure?
10. The bold carbon in each structure is called the  carbon. What is the hybridization of the 
carbon in each amino acid structure?
11. What are the approximate bond angles and the molecular geometry around the carbonyl carbon?
12. What are the approximate bond angles and the molecular geometry around the  carbon?
13. Orient your ball and stick model for alanine in the same view as the wedge-dash formula below.
Wedge-Dash Formula
Fischer Projection
Formula
14. Using the glutamate ball and stick model, manipulate the common functional groups around the
 carbon into a similar orientation as the alanine wedge-dash structure above. Draw a correct
Fischer projection formula for glutamate.
15. What do the horizontal bonds in the Fischer projection formula represent structurally?
16. What do the vertical bonds in the Fischer projection formula represent structurally?
17. Label the alanine structure above as the R or S stereoisomer. This is L-alanine.
18. Draw the Fischer projection for the other stereoisomer of alanine. Label this stereoisomer Dalanine.
19. Which stereoisomer, L-alanine or D-alanine, has the amino group on the left?
20. Draw the structure of L-valine and D-valine.
21. Of the four groups around the  carbon, the group that differs between the structures is called
the side chain, sometimes referred to as the R group. Compare the four side chains for the
amino acids in Model 1 and note at least three differences in the groups.