Biochemistry Introduction 1. Biochemistry The study of substances found in living organisms

1. Biochemistry Introduction 1. Biochemistry The study of substances found in living organisms and of changes they undergo during development and life of the organism - Chemistry of life 2. The course is divided into two parts Part I - Structural biochmeistry Part II - Dynamic biochemistry

2. Structural Biochemistry 1. Amino acids, Peptides, Proteins 2. Structure and function of proteins 3. Carbohydrates 4. Lipids 5. Biological membrane and transport 6. Nucleotides and nucleic acids 7. Enzyme 8. Enzyme catalysis

3. Dynamic Biochemistry 1. Introduction to metabolism 2. Glycolysis 3. The citric acid cycle 4. Oxidative phosphorylation 5. Gluconeogenesis, Pentose phosphate pathway, and Glycogen metabolism 6. Fatty acid catabolism 7. Lipid biosynthesis 8. Amino acid oxidation and production of urea 9. Biosynthesis of amino acids, nucleotides, and related molecules 10. Integration of metabolism

4. Amino Acids Introduction 1. G. J. Mulder in 1839 coined the term “protein” From Greek: proteios (meaning primary) 2. All proteins are composed of 20 “standard” amino acids 20 Commonly occurring amino acids - Building blocks of proteins Structure and Properties of Amino Acids 1. Anatomy of an amino acid α-Amino acid - α carbon Amino group Carboxylic group Side chain (R group)

5. 2. Amino acids can join via peptide bonds Condensation reaction Peptide - Dipeptide, Tripeptide, Oligopeptide - Polypeptide N-terminus, C-terminus, Amino acid residues - Protein 3. 20 standard amino acids Classification - R group - Nonpolar, Hydrophobic Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan - Polar, Uncharged Serine, Threonine, Asparagine, Glutamine, Cysteine

6. - Acidic Aspartate, Glutamate - Basic Lysine, Arginine, Histidine Three-letter code, One-letter code - Display protein sequence Glx, Asx 4. Uncommon amino acids Phosphoserine, Hydroxyproline, Methylhistidine, γ-Carboxyglutamate, ε-N-Acetyllysine 5. Amino acids not found in proteins Histamine, Dopamine, Thyroxine, γ-Aminobutyric acid (GABA)

7. Acid-Base Properties of Amino Acids 1. Weak polyprotic acids Zwitterion or dipolar ion Side Chains of Amino Acids Undergo Ionizations 1. α-Carboxyl group pKa (~ 2.2) 2. α-Amino group pKa (~ 9.4) 3. Side chain pKR 4. Isoelectric point pI

8. Optical and Stereochemical Properties of Amino Acids 1. Amino acids are chiral molecules α-Carbon - Asymmetric center, Chiral center (Greek: cheir, meaning hand) 2. Enantiomers Optical activity - Dextrorotatory, Levorotatory Diastereomers 3. Nomenclature D, L system - Absolute configuration Fischer convention - L-amino acids R, S system

9. Spectroscopic Properties of Amino Acids 1. Phe, Tyr, Trp Ultraviolet absorption spectrum - A280 2. Fluorescence 3. NMR spectra Separation and Analysis of Amino Acids 1. Chromatorgaphy Technique develpoed by Tswett Partition properties 2. Ion exchange chromatorgaphy Electrical properties Exchangers - Anion exchanger DEAE, QAE

10. - Cation exchanger CM Elution 3. Separation of common amino acids Moore*, Spackman, Stein* - 1972 Noble Price in Chemistry Amino acid analyzer