Amino AcidChemistry

Honors GeneticsLemon Bay High School

2017-2018

GoalsStudents should

Know the GENERAL STRUCTURE of an amino acid

Know that all amino acids differ only in the R-group/Side chain

Know there are 20 different biologically important amino acids

Know each CLASSIFICATION of amino acid

Know the amino acids that fit into each classification

Be able to identify each amino acid based on the R-group

STRUCTUREAll amino acids (except proline) have the same BASIC structure

• A carboxyl group (-COO-)

• An amino group (-NH3+)

• Side chain ("R-group") bonded

to the central carbon atom.

These carboxyl and amino groups

form peptide linkage.

Classification of Amino Acids

Classified according to the CHEMISTRY of the R-group/side

chain:

• Aromatic side chains (ring structures)

• Nonpolar/Hydrophobic side chains

• Polar/Hydrophilic side chains.

• Positive (Basic) side chains

• Negative (Acidic) side chains

Each category of side chain provides a different chemical

behavior for each amino acid that will determine HOW the final

protein product will FOLD.

Glycine is an

amino acid of

disagreement.

Some protein

chemists

describe it as

Polar, others

Nonpolar.

We will leave

it in the

Nonpolar

category.

Aromatic Side Chains

• Aromatic means “ring structure”

• Nonpolar and HYDROPHOBIC

• These amino acids will “cluster” in the center of the folded

protein.

• Tyrosine is an important in some enzymes.

• A property exploited by researchers in the characterization of

proteins.

Nonpolar Side Chains

• These side chains are HYDROPHOBIC

• Remember, HYDROPHOBIC means they are insoluble in

water.

• Because of this, they “cluster” in the center of the folded

protein.

• Special amino acids in this group

Glycine – the smallest side chain

The smallest side chain

Has both Polar and Nonpolar properties

Proline

Forms a ring structure that incorporates the central carbon in the constant region

Provides the fibrous structure of collagen

Polar Side Chains

• These side chains are HYDROPHILIC

• Remember, HYDROPHILIC means they are soluble in water because they form hydrogen bonds with water.

• Because of this, they will remain on the outer margins of the folded protein.

• Cysteine contains a sulfhydryl group (-SH), an important component of the active site of many enzymes.

Cysteine is important in the folding process – it wants to form a bridge of bonds with another cysteine amino acid

Basic Side Chains• These side chains have a significant positive charge

• The pH of the fluid surrounding the protein will influence the

behavior of these amino acids

At neutral pH, these amino acids are fully ionized (+)

Fluctuations of pH can alter the 3D fold of a protein by interrupting this ionization.

• These side chains want to form ionic bonds within the protein

with acid side chain amino acids

Acidic Side Chains

• These side chain have a significant negative charge

• The pH of the fluid surrounding the protein will influence the behavior of these amino acids At neutral pH, these amino acids are fully ionized (-)

Fluctuations of pH can alter the 3D fold of a protein by interrupting this ionization.

• These side chains want to form ionic bonds within the protein with base side chain amino acids