3-1 AMINO ACIDS
Introduction

The study of amino acids will help biochemists to further understand the structure and
function of _______________.

The study of proteins may lead to understanding the keys to some of the most pressing
scientific challenges.
o How does photosynthesis work? How can we synthetically replicate it to help
meet our energy needs?
o How do some bacteria live, or even thrive, at temperatures greater than 100°C
(called thermophilic bacteria) when most proteins at this temperature are
destroyed?
o How can we predict mutations of viruses and create effective treatments before
these mutations even form?
Biological Functions of Proteins
1. _______________ - Biochemical catalysts.
2. Bind other molecules for _______________ and _______________.
3. Provide _______________ and _______________ to cells, therefore tissues and
organisms.
4. Complete _______________ work (movement of flagella, separation of chromosomes
during mitosis, and contraction of muscles).
5. _______________ information in the cell (translation, regulating gene expression).
6. _______________ - regulate biochemical activities in target cells or tissues. Some are
_______________ for these.
7. Other highly _______________ functions (antibodies, toxins, etc.).
General Structure of Amino Acids

Grab a partner and two molecular model kits, and follow the instructions below!
1. Assemble a generic amino acid, leaving the “R” group as an empty bond and ignore any
ionization at this point. Draw it below using wedge-and-dash notation (wedge – out of
the plane of the paper, dash – into the plane of the paper).
2. Attach a methyl group as the R group. Name this using the IUPAC system of
nomenclature.
3. Name the molecule using the old, trivial name. In the old system, the carbon with the R
group attached is known as the alpha () carbon. This is carbon #___ in the IUPAC
system. Carbons 3 – 6 receive the symbols and
4. In the physiological pH range (6.8-7.4), the amino group is protonated and the carboxyl
group is ionized. Make this change to your alanine molecule and redraw it below. The
molecule now has a positive formal charge on the N and a negative formal charge on one
of the O atoms. It is called a _______________, or a dipolar ion.
5. In 19 of the 20 amino acids, the –carbon is _______________ (asymmetric – has four
different groups bonded to it). Identify the only amino acid that does not have a chiral –
carbon.
6. The 19 chiral amino acids can exist as _______________ – compounds that have the
same molecular formula but differ in the arrangement of their atoms in space. Two
stereoisomers cannot easily be converted from one to the other because it requires the
breaking of one or more _______________.
7. Build another alanine molecule, but make them nonsuperimposable mirror images.
These are called _______________. Draw them below with the carboxyl group pointing
up and away, and the “R” group pointing down and away. If the -amino group is on the
left, then the isomer is the “L” isomer. If the -amino group is on the right, then it is the
“D” isomer. Label your enantiomers of alanine L and D by putting these letters in front
of the name separated by a dash.
8. The 19 chiral amino acids used in the assembly of proteins are all of the ___
configuration. This is evidence that all species on Earth are descended from a common
_______________. It is unknown how or why primitive life forms chose L-amino acids
over D-amino acids in the presumed _______________ mixture available. Both
enantiomers are found in meterorites and in the vicinity of stars. The predominance of Lamino acids in modern species is due to the evolution of metabolic pathways that produce
L-amino acids and not D-amino acids.
Hydrophobicity of Amino Acid Side Chains

The hydrophobicity or hydrophilicity of an amino acid is called its _______________.
Amino acids are rated on a hydropathy scale (Table 3.1). Hydropathy helps to determine
how proteins will __________. _______________ side chains will be clustered in the
interior of proteins where _______________ are usually found on the surface.