ST. JOHN’S UNIVERSITY NEW YORK
DEPARTMENT OF PHARMACEUTICAL SCIENCES COURSE SYLLABUS FOR BIOCHEMISTRY AND BIOTECHNOLOGY
PHS 2201
SPRING SEMESTER 2ND YEAR
Syllabus for Biopharmaceutical Chemistry
1. Course Description:
The course is an intermediate level undergraduate biochemistry and molecular biology lecture course. The chemistry of macromolecules, i.e., proteins, lipids assemblies, nucleic acids, and polysaccharides, enzymology, an introduction to metabolic pathways and energy utilization in cells is the bulk of the material. In addition, the fundamental biochemical notions of nucleic acid metabolism, including DNA replication and repair mechanisms, RNA, and protein synthesis is covered. Vitamins and trace metals are discussed from the standpoint of their role in enzymatic reactions and metabolic sequences, and where possible related to health consequences.
2. Objectives:
Provide fundamentals of biochemistry and molecular biology to pharmacy students. Biochemistry fundamentals include structure and function of macromolecules, of enzyme action, an introduction to the concept of metabolic pathways, introduction to the major energy linked pathways, and bioenergetics. Molecular biology fundamentals include essential chemistry of DNA and RNA, enzymology of replication, transcription, and translation, interactions between nucleic acids and other macromolecules and small molecules, and regulatory influences understandable from known chemical interactions.
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3. Course Outline:
Lecture hrs. Supplementary Assign hrs.
Week One 10 10 Week Two 10 10 Week Three 10 10 Week Four 10 10 Week Five 10 10 TOTAL 50 50
Week One
Introduction Definition of biochemistry as chemistry of life processes Cellular organization Water The significance of water for biological systems Water structure Meaning of pH and pK The Hendersson-Hasselbach Equation
Lipids Major structural classes of lipids Lipid-water interactions: the importance of interface The hydrophobic effect The eicosanoids: Prostaglandins and leukotrienes Other lipid-related signal molecules
Carbohydrates Structural elements of carbohydrates Types of monosaccharides Stereochemistry Ring forms and open chain forms of sugars Derivatives of carbohydrates Glycosides and glycosidic linkage Disaccharides and Oligosaccharides Polysaccharides
Proteins I: Introduction to Proteins Amino Acids Chemical categories of amino acids
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Practice exam #1 Assignment #1: Molecular models of Organic Structures, Lipids, Carbohydrates and Aminoacids
Week Two
Proteins II: Acid-base properties and their relation to molecular charge The peptide bond Oligopeptides Examples of peptides: hormones and antibiotics
Proteins III: Three Dimensional Structure of Proteins Levels of structure from primary to quaternary Secondary structure Tertiary structure Quaternary structure Protein folding and denaturation Myoglobin and Hemoglobin Immunoglobulins
Introduction to Nucleic Acids Bases, Nucleosides and Nucleotides Polynucleotides DNA RNA Practice exam #2 Assignment #2: Use of Protein Databases
Week Three
Proteins IV: Enzymes The six classes of enzymes The coenzymes A simple kinetic mechanism for enzyme action Analysis of the Michaelis-Menten Equation Vmax and Km Reversible Inhibitors Irreversible inhibitors Chemistry of enzyme mechanism The transition state Acid-base catalysis
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Allosteric enzymes Allosterism in Hemoglobin Covalent modification of enzymes: signal systems and cascades
Bioenergetics and transport Membrane Transport Facilitated Diffusion and Active transport Metabolism and energy, principles of metabolic pathways Free energy: the combination of the two laws of Thermodynamics Energy coupling with ATP
Practice exam #3 Grade exam #1 Assignment #3: Data processing in enzyme kinetics
Week Four
Carbohydrate metabolism Glycolysis Overview to glycolysis, a metabolic pathway Lactate formation Ethanol formation Energetics of Glycolysis The pentose phosphate pathway Sucrose and lactose catabolism Glycogen Metabolism and Related Pathways Gluconeogenesis
Intermediary metabolism Citric Acid Cycle Carbon flow through the Krebs Cycle Energy flow in the Krebs Cycle Regulation of the Krebs Cycle The Electron transport chain: respiratory complexes Oxidative Phosphorylation Uncoupling Shuttle pathways for cytosolic NADH oxidation
Lipid Metabolism Dietary absorption of lipids Fatty acid oxidation Fatty acid biosynthesis Biosynthesis of the neutral lipids Membrane lipid biosynthesis
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Steroid Metabolism
Nitrogen Metabolism Nitrogen metabolism, amino acids and proteins Patterns of amino acid metabolism The urea cycle Balance of nitrogen for the urea cycle Amino acids as metabolic precursors to drugs Metabolic origin of the alkaloids
Nucleotide metabolism Catabolism of purine and pyrimidine nucleotides Purine salvage Nucleotide biosynthesis Deoxynucleotide biosynthesis
Practice exam #4 Assignment #4: Problems on metabolism
Week Five
The Central Dogma of Molecular Biology
DNA Replication DNA Repair and Recombination Damage to DNA: Mutation
Transcription: Biosynthesis of RNA Control processes in bacterial and eukaryotic transcription RNA processing
Protein Synthesis The genetic code Ribosomes Mechanics of Translation Inhibitors of Translation
Practice exam #5 Grade exam #2 Grade Improvement exams
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4. Criteria for evaluation
Exams will be used to provide the grade for the course, with the scale.
There will be a practice exam every week. The practice exams consist in multiple- option quizzes (only one option true) of fifteen questions (2 attempts) to be done on- line.
The grade will result from the weighted mean of two exams: One covering Weeks #1 and #2 (20 questions quiz, 1 attempt) and the other covering Weeks #3, #4 and #5 (30 questions quiz, 1 attempt) to be done in the classroom.
The correspondence between grades is:
Sp.grade St.John’s grade
9.3-10.0 A 9,0-9.29 A- 8.7-8.99 B+ 8.3-8.69 B 8.0-8.29 B- 7.7-7.99 C+ 7.3-7.69 C* 7.0-7.29 C-* 6.7-6.99 D+ 6.0-6.69 D** Below 6.0 F
*For many visiting students (i.e., non-STJ students studying on the STJ program, a “C” or “C+” is the lowest grade they can transfer for credit at their home institutions)
**For STJ students, a “D” is the lowest grade they can receive and still receive academic credit.
5. Bibliography
Text
Principles of Biochemistry, 211 Edition, Horton, Moran, Ochs, Rawn, Scrimgeour, 2005, Prentice Hall
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Aside from the text, other current biochemistry texts may be used as references such as Biochemistry, Voet and Voet, 2nd Edition, Wiley, 1995 and Schaum Outline for Biochemistry, McGraw-Hill, 1988, Lippincott’s Illustrated Reviews, Campe and Harvey, 2nd Edition, 1994
6. Other Materials
All the study material of the course will be posted at the STUDIUM page of the virtual campus of Universidad de Salamanca. Usernames and passwords will be provided for all the students.
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