Biochemistry Free For All

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Presentation transcript:

Biochemistry Free For All Amino Acids Biochemistry Free For All

Part 1 - Amino Acids Building Blocks of Proteins Essential Amino Acids Structure and Chemistry Building Blocks of Proteins Essential Amino Acids Basic Structure Stereochemistry Side Chain Chemistry Properties Ionization Bonding

Proteins comprised of 20-21 amino acids Amino Acids & Proteins Workhorses of cell Catalysis Signaling Structure Energy/Gradient Generation Proteins comprised of 20-21 amino acids

Amino Acids Essential Amino Acids

Basics of Structure Alpha Carbon Alpha Carboxyl Alpha Amine Elements Alpha Amino Acids Differences in R Groups Alpha Amine

R Basics of Structure Alpha Carbon Alpha Carboxyl Alpha Amine Asymmetric Center Alpha Carboxyl Elements Alpha Amino Acids Differences in R Groups Examples Alpha Amine Alpha Carbon Alpha Carboxyl Alpha Amine R

R Basics of Structure Alpha Carbon Alpha Carboxyl Alpha Amine Asymmetric Center Alpha Carboxyl Elements Alpha Amino Acids Differences in R Groups Examples Alpha Amine R 18 Alpha Amine Alpha Carbon Alpha Carboxyl

Amino Acids Asymmetric Carbon Almost all biological amino acids Stereochemistry D and L Isomers Almost all biological amino acids are in the L-configuration

Categorizing Amino Acids Non-Polar Carboxyl Amine Aromatic Hydroxyl Other Alanine Aspartic Acid Arginine Phenylalanine Serine Asparagine Glycine Glutamic Acid Histidine Tryptophan Threonine Cysteine Isoleucine Lysine Tyrosine Glutamine Leucine Selenocysteine Methionine Pyrrolysine Proline Valine

Approximate R-group pKa Ionizable R-groups Name Charged R-group Approximate R-group pKa Glutamic Acid -COO- 4.1 Histidine -NH3+ =NH2+ =-NH+ 6.0 Cysteine -S- 8.2 Tyrosine -O- 10.5

Amino Acids Alpha Carboxyl Alpha Carbon Alpha Amine Tryptophan Aromatic R-Groups Alpha Carboxyl Alpha Carbon Alpha Amine Tryptophan Tyrosine Phenylalanine

Amino Acids R Aromatic R-Groups Tryptophan Tyrosine Phenylalanine

Amino Acids R Tryptophan Ionizes at high pH Tyrosine Phenylalanine Aromatic R-Groups Charges at Physiological pH Tryptophan Ionizes at high pH Tyrosine Phenylalanine

Amino Acids Leucine Proline Alanine Glycine Isoleucine Valine Aliphatic R-Groups Leucine Proline Alanine Glycine Isoleucine Valine Methionine H

Amino Acids Leucine Proline Alanine Glycine Isoleucine Valine Aliphatic R-Groups Leucine Proline Alanine Glycine Isoleucine Valine Methionine H

Amino Acids Aliphatic R-Groups Charges at Physiological pH

Amino Acids R-Group Carboxyls Aspartic Acid Glutamic Acid

Amino Acids R-Group Carboxyls R Aspartic Acid Glutamic Acid

R R Amino Acids Aspartic Acid Glutamic Acid R-Group Carboxyls Charges at physiological pH R R Aspartic Acid Glutamic Acid

Amino Acids Hydroxyl R-Groups Serine Threonine Tyrosine

Amino Acids Hydroxyl R-Groups Serine Threonine Tyrosine

Amino Acids Serine Threonine Ionizes at high pH Tyrosine Hydroxyl R-Groups Charges at Physiological pH Serine Threonine Ionizes at high pH Tyrosine

Amino Acids Sulfhydryl R-Group Cysteine

Amino Acids Sulfhydryl R-Group Ionizes at about pH = 8 + Cysteine

Amino Acids Carboxamide R-Groups Asparagine Glutamine

Amino Acids Carboxamide R-Groups Asparagine Glutamine

Amino Acids Carboxamide R-Groups Asparagine Glutamine

Amino Acids Ionizable Amine R-Groups Lysine Arginine Histidine

Amino Acids Ionizable Amine R-Groups Lysine Arginine Histidine

Amino Acids Arginine Lysine Histidine Ionizable Amine R-Groups Charges at Physiological pH Lysine Arginine Histidine

Rare Amino Acids

Non-Protein Amino Acids Carnitine Also - Citrulline, Ornithine, others

Amino Acids Ionization

Amino Acids Ionization -by pKa Values

Amino Acids Ionization -by pKa Values

Amino Acids Ionization -by pKa Values

Amino Acids Ion Locations in Titration Charge = -1

Amino Acids Ionization -by pKa Values Charge = 0

Amino Acids Ionization -by pKa Values Charge = -1

Amino Acids Ionization -by pKa Values Charge = -2

Ionization Changes Charges Within Proteins Changes in Charge Change Activities

Post-translational Modifications

Phosphorylated Amino Acids

Breakdown of Amino Acids

Peptide Bond Formation