Arik Dvir - Biochemistry
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BIO 325: Biochemistry I (4 credits)

The course reviews the basic principles of organic chemistry and molecular biology that are given in introductory courses- properties of carbon compounds and functional groups; covalent and non-covalent interactions; and principles of thermodynamics, and builds on this knowledge to understand the structure and function of the major classes of macromolecules. The course gives emphasis to principles of enzyme's action and regulation, with consideration of structure/function relationships and quantitative analysis. The last section of the course is an introduction to intermediary metabolism, covering both metabolic pathways and principles of regulation and energy considerations. We examine the metabolic pathways of glycolysis, gluconeogenesis, citric acid cycle; oxidative phosphorylation; and glycogen metabolism.

List of topics:

  • The scope of biochemistry
  • Principles of thermodynamics
  • Water properties and non-covalent interactions
  • Carbon compounds
  • Lipids
  • Carbohydrates
  • Nucleic acids
  • Proteins
  • Analytical and quantitative methods in biochemistry
  • Principles of enzyme action: Enzyme mechanisms
  • Principles of enzyme action: Quantification of enzyme activity
  • Principles of enzyme action: Regulatory mechanisms
  • Principles of enzyme action: co-enzymes
  • Principles of intermediary metabolism
  • Glycolysis
  • Gluconeogenesis
  • Krebs cycle
  • Oxidative phosphorylation
  • Glycogen metabolism

Textbook: Lehninger's Principles of Biochemistry, 3rd edition by Nelson and Cox.

BIO 326: Biochemistry I Lab (1 credit)

This lab course is particularly suitable for students who take or plan to take Biochemistry I (Bio 325 or equivalent), or for students with solid background in chemistry and molecular biology who are interested in practical experience in protein biochemistry and enzymology. All lab sessions are focused on a single subject- purification and characterization of a yeast enzyme- invertase. The course includes methods for analysis and quantification of enzymatic activity, bulk fractionation procedures including salting-out and organic extraction, and chromatographic procedures such as electrophoresis and ion exchange. Emphasis is given to the management and documentation, analysis, and presentation of collected data. The grade is based on quizzes (30%), organization during the lab (20%) and lab reports (50%).

Session 1 (class): Introduction
Session 2 (lab): Nelson assays for glucose: calibration curve and enzyme kinetics.
Session 3 (lab): Substrate kinetics, inhibitors.
Session 4 (class): Summary and analysis of kinetic experiments
Session 5 (lab): Extraction and partial purification of invertase from yeast cells.
Session 6 (lab): Enzyme activity assays.
Session 7 (lab): Protein assay.
Session 8 (class): Summary and data analysis (including specific activity and yield calculations).
Session 9 (lab): Ion Exchange Chromatography.
Session 10 (lab): Ion Exchange: Nelson assays, protein assays.
Session 11 (lab): Gel-Electrophoresis
Session 12 (class): Last meeting and summary; analysis of ion exchange and gel-electrophoresis results.

BIO 425: Biochemistry II (4 credits)

In this course we continue the study of metabolism that we began in Biochemistry I (Bio 325), with the addition of several special-interest topics. Students are required to give one presentation on a topic of their choice from the course materials, in addition to exams. Special attention is given to mechanistic aspects of enzyme and cofactor function. Offered winter semester. Prerequisites: Bio325 or equivalent.

Detailed topic list:

Glycogen metabolism
Regulation of glucose metabolism
Fatty acid metabolism
Cholesterol metabolism
Amino acid metabolism
Signal transduction
Metabolic coordination in vertebrates
Structure of nucleic acids and nucleoproteins
Gene expression - protein-DNA interactions
Gene expression - basal transcription in eukaryotes
Gene expression - activated transcription in eukaryotes

Textbook: Lehninger's Principles of Biochemistry, 3rd edition by Nelson and Cox.

Comments? Questions? Contact Dr. Dvir.