Overview of Protein Synthesis in
Eukaryotic Cells
→ DNA is transcribed to form messenger RNA
(mRNA) in the nucleus
→ mRNA is exported to the cytoplasm
→ mRNA is translated into a linear sequence of
amino acids that folds into a 3D structure
→ Protein function is determined by protein
structure, which is determined, in turn, by
the structures and properties of the various
amino acids that make up the protein.
→ Any diseases are a consequence of amino
acid mutations that render a protein
unstable, or nonfunctional.
Amino Acids
Structure of the α-Amino Acids
An amino acid has
– α-Carbon is central to an amino acid
– amino group
– carboxyl group
– side chain(R group), amino acid-specific group
At neutral pH (~7) the amino acid nitrogen is
protonated and the carboxylic acid is deprotonated to
yield the zwitterion.
The non-ionic form does not occur in significant
amounts in aqueous solutions.
→ A molecule having a net formal charge of zero, but
negative and positive charges on individual atoms
within its structure
→ All α-amino acids (20), except glycine, contain an
asymmetric α-carbon
→ L-alanine is the mirror image of ᴅ-alanine
→ L-alanine and ᴅ-alanine are enantiomers
Stereoisomers~ are known as non-superimposable
TJW NOTES mirror images of one another –also known as
enantiomers.
, Stereochemistry of the α-Amino Acids
→ L-form amino acids are the most common in
naturally occurring proteins
→ The stereochemistry of the amino acids is a major
determinant of the structure of proteins.
→ The asymmetry of protein binding sites determines
which small molecules they will bind.
→ Thus, the efforts of medicinal chemists to design
new drugs include matching the shape of the drug
to that of the binding site in the target protein.
TJW NOTES
, Properties of Amino Acid Side Chains: Classes of α-Amino Acids
The variety of side chains on amino acids allows proteins enormous versatility in structure and function.
Amino Acids with Nonpolar Aliphatic Side Chains
• Glycine, alanine, valine, leucine, and isoleucine have aliphatic side chains
• The more hydrophobic amino acids such as isoleucine are usually found within the core of a folded protein
molecule, where they are shielded from water.
• Isoleucine R = −CH CH3 CH2 CH3 has a much greater tendency to transfer from water to a
hydrocarbon solvent than alanine R = −CH3 does.
• Glycine R = −H is difficult to fit into any category. Although its side chain has aliphatic character, it is
frequently found on the surfaces of proteins due to its ability to form tight turns in protein structures. Such
turns are sites in the protein structure where the protein polymer folds back on itself.
• Proline, which has a secondary α-amino group, is also difficult to classify. It is the only amino acid in this
group in which the side chain forms a covalent bond with the α-amino group.
• The proline side chain has a primarily aliphatic character, but, like glycine, it is frequently found on the
surfaces of proteins because the rigid ring of proline is well suited to turns.
• Methionine R = −CH2 CH2 SCH3 in this group even though it is not technically an aliphatic amino acid.
Because sulfur has the same electronegativity as carbon, the thioether side chain is quite hydrophobic; thus,
methionine displays many of the same properties as the other nonpolar amino acids.
TJW NOTES
Eukaryotic Cells
→ DNA is transcribed to form messenger RNA
(mRNA) in the nucleus
→ mRNA is exported to the cytoplasm
→ mRNA is translated into a linear sequence of
amino acids that folds into a 3D structure
→ Protein function is determined by protein
structure, which is determined, in turn, by
the structures and properties of the various
amino acids that make up the protein.
→ Any diseases are a consequence of amino
acid mutations that render a protein
unstable, or nonfunctional.
Amino Acids
Structure of the α-Amino Acids
An amino acid has
– α-Carbon is central to an amino acid
– amino group
– carboxyl group
– side chain(R group), amino acid-specific group
At neutral pH (~7) the amino acid nitrogen is
protonated and the carboxylic acid is deprotonated to
yield the zwitterion.
The non-ionic form does not occur in significant
amounts in aqueous solutions.
→ A molecule having a net formal charge of zero, but
negative and positive charges on individual atoms
within its structure
→ All α-amino acids (20), except glycine, contain an
asymmetric α-carbon
→ L-alanine is the mirror image of ᴅ-alanine
→ L-alanine and ᴅ-alanine are enantiomers
Stereoisomers~ are known as non-superimposable
TJW NOTES mirror images of one another –also known as
enantiomers.
, Stereochemistry of the α-Amino Acids
→ L-form amino acids are the most common in
naturally occurring proteins
→ The stereochemistry of the amino acids is a major
determinant of the structure of proteins.
→ The asymmetry of protein binding sites determines
which small molecules they will bind.
→ Thus, the efforts of medicinal chemists to design
new drugs include matching the shape of the drug
to that of the binding site in the target protein.
TJW NOTES
, Properties of Amino Acid Side Chains: Classes of α-Amino Acids
The variety of side chains on amino acids allows proteins enormous versatility in structure and function.
Amino Acids with Nonpolar Aliphatic Side Chains
• Glycine, alanine, valine, leucine, and isoleucine have aliphatic side chains
• The more hydrophobic amino acids such as isoleucine are usually found within the core of a folded protein
molecule, where they are shielded from water.
• Isoleucine R = −CH CH3 CH2 CH3 has a much greater tendency to transfer from water to a
hydrocarbon solvent than alanine R = −CH3 does.
• Glycine R = −H is difficult to fit into any category. Although its side chain has aliphatic character, it is
frequently found on the surfaces of proteins due to its ability to form tight turns in protein structures. Such
turns are sites in the protein structure where the protein polymer folds back on itself.
• Proline, which has a secondary α-amino group, is also difficult to classify. It is the only amino acid in this
group in which the side chain forms a covalent bond with the α-amino group.
• The proline side chain has a primarily aliphatic character, but, like glycine, it is frequently found on the
surfaces of proteins because the rigid ring of proline is well suited to turns.
• Methionine R = −CH2 CH2 SCH3 in this group even though it is not technically an aliphatic amino acid.
Because sulfur has the same electronegativity as carbon, the thioether side chain is quite hydrophobic; thus,
methionine displays many of the same properties as the other nonpolar amino acids.
TJW NOTES
