3-2 STRUCTURES OF THE 20 COMMON AMINO ACIDS
1. Assemble a generic amino acid using a molecular model kit. Leave the “R” group as a bond
without an atom attached. Hold the molecule so that the carboxyl group is on top and back, and
the amino group is on the left and forward. In Fischer projections, horizontal bonds at a chiral
center extend toward the viewer (wedges) and vertical bonds extend away (dashes). Draw L- and
D- versions of a generic amino acid as wedge and dash depictions, and as Fischer projections.
2. The properties of the side chains greatly influence the _______________ (3D shape) of a protein.
The structures, three-letter and one-letter abbreviations must be put to memory because they will
be used frequently in the chapters on protein structure, enzymes, and protein synthesis.
Amino Acids with Aliphatic R Groups
3. Assemble glycine, alanine, valine, leucine and isoleucine. Draw them below in their Lconformation using Fischer projections. Place their abbreviations with them.
4. Which of the above amino acids plays a unique role in the structure of many proteins because its
side chain is small enough to fit into niches that can accommodate no other amino acid?
5. The other four aliphatic amino acids have _______________ aliphatic side chains, which play
important roles in establishing and maintaining the 3D structures of proteins because they have a
tendency to cluster away from __________. Which three are branched-chain amino acids?
6. Construct proline, draw its Fischer projection and give it its abbreviations.
7. Proline is unique in the fact that its side chain forms a _______________ ring, which reduces its
_______________, and restricts the _______________ of polypeptides. This can sometimes
cause abrupt changes in _______________ of the peptide chain.
Amino Acids with Aromatic R Groups
8. Construct a benzene ring with a model kit. You will probably need a second kit, but please make
sure you put the right numbers of atoms back in their original kits! With the benzene ring,
construct phenylalanine, then tyrosine, then tryptophan. Draw their Fischer projections below,
and label them with their names and one-letter abbreviations.
9. Which of the amino acids above would be the most hydrophobic?
10. These three aromatic amino acids absorb _______________ light because they contain
delocalized -electrons. Tryptophan and tyrosine absorb light at 280 nm, where phenylalanine
weakly absorbs light at 260 nm. Absorbance at 280 nm is routinely used to estimate the
_______________ of proteins in solution.
Amino Acids with Sulfur-Containing R Groups
11. Construct methionine and cysteine, draw their Fischer projections below, and label them with
their names and their one-letter abbreviations.
12. Which of these is one of the more hydrophobic amino acids, and is almost always the first amino
acid in a polypeptide chain?
13. Write an equation showing the formation of a disulfide bridge between two cysteine residues.
14. The product is known as cystine. Disulfide bonds can form between two cysteine side chains that
are _______________ to each other, and they may _______________ the 3D structures of some
proteins by cross-linking cysteine residues in peptide chains.
Amino Acids with Alcohol Groups
15. Construct serine and threonine, draw their Fischer projections below, and label them with their
names and their one-letter abbreviations.
16. Both of these amino acids have ___-hydroxyl groups, providing them with _______________
character. These can weakly ionize like primary and secondary alcohols, and they can react
within the active sites of a number of enzymes.
Amino Acids with Basic R Groups
17. Construct histidine, lysine and arginine, draw their Fischer projections below, and label them with
their names and their one-letter abbreviations.
18. The side chains of these amino acids are _______________, and are _______________ charged
at pH of 7. Histidine’s side chain contains an _______________ ring, and is called an
_______________ ion when it is protonated. Lysine is a _______________ acid, having amino
groups at the ___ and ___ carbons. _______________ is the most basic of the 20 amino acids
because its side chain _______________ ion is protonated under all conditions normally found
within a cell.
Amino Acids with Acidic R Groups
19. Construct aspartate, glutamate, asparagine, and glutamine, draw their Fischer projections below,
and label them with their names and their one-letter abbreviations.
20. Aspartate and glutamate are _______________ acids, but are _______________ at pH of 7.
Glutamate is familiar as its monosodium salt, _______________ _______________ (MSG), used
in food as a _______________ enhancer.
21. _______________ and _______________ are highly _______________ and are found at the
surface of proteins where they can interact with water.
Other Amino Acids

There are more than __________ different amino acids found in living organisms.

All species contain a variety of L-amino acids.

o
They can be _______________ of the common amino acids.
o
They can be _______________ in other biochemical pathways.
Several common amino acids are chemically modified to produce biologically important
_______________ through decarboxylation and deamination.

Some amino acids are chemically modified __________ they’ve been incorporated into
polypeptides.

A 21st and a 22nd amino acid have been discovered as well. One is formed from serine during
protein synthesis, and the other is a derivative of lysine that is synthesized before being added to a
growing polypeptide chain by the translation machinery. Draw Fischer projections of these
molecules below.

Read section 3.3 for many examples of where other amino acids play roles in biochemical
processes.