Course Outline: Advanced Biochemistry (CHM381)

Course Information

Credits: 3

Contact Hours:

• Lecture: 3

Semesters Offered: Fall, Spring, & Summer

Prerequisites: CHM271 and CHM380

Catalog Course Description:

A continuation of the concepts covered in Biochemistry. Students will examine the pathways, enzymes, and organic chemical mechanisms involved in the metabolic pathways of carbohydrates, lipids, amino acids, nucleic acids, and photosynthesis. Additional emphasis will be placed on the unique coenzymes that are required for these metabolisms. Students will also be trained in reading and interpreting research publications in biochemistry.

Elective Course for: Bioscience

Course Texts: John McMurray, Tadhg Begley. The Organic Chemistry of Biological Pathways. Englewood, Colorado: Roberts & Company, 2005

Course Learning Objectives

I. Biochemistry Review

Categories of biomolecules, characteristics of metabolic pathways, enzyme categories, fundamental enzyme mechanisms.

At the end of this section, the student should be able to:

1. Identify by name and structure the four major categories of biomolecules
2. List and define the four characteristics of metabolic pathways
3. List, define, and identify the six categories of enzymes
4. List and efine the four fundmental enzyme mechanisms

II. Organic Chemistry Review

Lewis Acid / Base theory, fundamentals of organic reactions, acidity of the alpha carbon to carbonyls, drawing and interpreting electron pushing mechanisms

At the end of this section, the student should be able to:

1. Identify compounds as Lewis acids or bases
2. Identify nucleophiles and electrophiles in organic reactions
3. Predict the product of biochemically relevant organic reactions
4. Predict the most probable mechanism and draw the electron pushing
5. Draw the tautomerization of a ketone 

III. Carbohydrate Metabolic Pathways 

Glycolysis, Gluconeogenesis, Pyruvate Dehydrogenase, Glyoxylate shunt, Citric Acid Cycle, Glycogen, Pentose Phosphate pathways.

At the end of this section, the student should be able to:

1. Assemble all intermediate structures and names in proper order in the glycolysis/gluconeogenesis and citric acid cycle pathways
2. Draw the mechanism for each metabolic conversion within the given pathways
3. Draw the mechanism for the cofactors thiamine pyrophosphate, flavin adenine dinucleotide, nictoinamide adenine dinucleotide and nictoinamide adenine dinucleotide phosphate
4. Describe the methodologies used to distinguish between a one-step or two-step phosphate transfer reaction

IV. Lipid Metabolism

β-Oxidation, fatty acid synthesis, odd chain fatty acid metabolism, glycerol synthesis, sphingosine synthesis, prostaglandin synthesis, synthesis of cholesterol from isoprenes 

At the end of this section, the student should be able to:

1. Assemble all intermediate structures and names in proper order in the fatty acid β-oxidation/synthase, glycerol synthesis,  and sphingosine synthesis pathways
2. Draw the mechanism for each metabolic conversion within the given pathways
3. Draw the mechanism for the cofactors heme and adenosylcobalamin. 

V. Amino acid Metabolism

Anabolism and catabolism of amino acids, deamination and 

transamination, urea cycle, glucogenic vs. ketogenic, essential and nonessential amino acids. 

At the end of this section, the student should be able to:

1. Assemble all intermediate structures and names in proper order in the urea cycle. 
2. Predict the result of a deamination on an amino acid
3. Draw the mechanism for important metabolic steps within the given pathways
4. Draw the mechanism for the cofactors pyridoxyl phosphate, folate, S-adenosylmethionine, and methylcobalamin. 
5. Define  and identify glucogenic and ketogenic amino acids
6. Identify all amino acids as either essential or nonessential.
7. Identify and assemble an abbreviated pathway including important intermediates for all amino acid anabolisms and catabolisms

VI. Nucleic Acid Metabolism

Anabolism and catabolism of nucleic acid bases, fate of purine bases after catabolism, ribonucleotide reductase

At the end of this section, the student should be able to:

1. Reproduce the metabolic pathways and mechanisms for anabolism of all four major bases from amino acid precursors. 
2. Reproduce the metabolic pathways and mechanisms for catabolism of all four major bases and their ultimate fate in the body.
3. Draw the mechanism for both types of ribonucleotide reductase enzymes

VII. Photosynthesis and Calvin Cycle

VIII. Literature Reading and Interpretation

Light reactions, chlorophyll, photosytem I & photosystem II, water splitting, Calvin cycle, metabolic controls on photosynthesis

At the end of these sections, the student should be able to:

1. Read a scholarly journal article and determine the main point
2. State the question, define the experiment and controls, and state the conclusions of each experimental figure in said paper.
3. Present the paper in front of a small group, demonstrating their grasp of the paper and their ability to convey that to the group.

NOTE: This course outline supersedes any course syllabus provided by a professor.