Questions and Sequence of Topics
- Why Do We Get the Flu Every Year?
- How Do Large Organic Molecules Bind to One Another?
What Makes Carbohydrates Information Rich?
- How Do Cells Recognize Things?
Introduction
- The Nature of the Question
- Biomolecular Recognition
- Relative Sizes and Energies
- Non-Covalent Interactions: H-Bonding and p-Stacking
- Importance of Carbohydrates as Information Carriers
Background and Review
- The Functional Groups: Aldehydes, Alcohols, Ketones, Carboxylic Acids, Amines, and Amides
- Hemiacetal and Acetal Chemistry
- Stereoisomers: Chirality and Conformational Analysis
Carbohydrates
- Basic Structure and Nomenclature - Aldose and Ketose Sugars
- Stereochemistry
- Rings
Haworth Projections and Pyranose Conformations
Ring Formation and Opening
a- and b-Anomers
- Important Monosaccharides
Glucose, Galactose, Mannose, Ribose, N-Acetylglucosamine, Sialic Acid
Reactivity - Glycosides (methanol and serine), Acetylation, Borate Esters, Phosphorylation, Acetonides (?), Redox (?)
Biosynthesis of Sialic Acid
- Di-, Oligo-, and Polysaccharides
Linkages Between Monosaccharides
Lactose, a Branched Pentasaccharide, Starch, Cellulose, Glycogen
Methodologies for the Structure Elucidation of Carbohydrates
Amino Acids and Proteins
- Amino Acids
Structure, Nomenclature, and Chirality
Importance of Side Chains as Recognition Sites
- Reactivity and Synthesis
Acid-Base Properties
Amide and Peptide Formation, Synthesis
- Polypeptides and Proteins
Primary, Secondary, and Tertiary Structures
- Glycoproteins
Occurence and Types of Linkages
Cell-Surface Carbohydrates
Virus-Cell Recognition
- Structure of Viruses and the Cell-Recognition Process
- Non-Covalent Interactions
- Why We Get The Flu Every Year?
- Challenges for the Future
Student Outcomes and Learning Strategies
Student Outcomes
Content
- Carbohydrate Structure and Reactivity
- Amino Acid and Protein Structure and Reactivity
- Biomolecular Recognition of Carbohydrates and Proteins
Skills
- Formulating Questions
- Dealing with Polyfunctional Organic Molecules
- Deciphering the Basic Structures of Carbohydrates and Amino Acids
- Predicting the Reactivity of Sugars and Amino Acids
- Making Sense of the 3-Dimensional Images of Complex Molecules
- Developing Teamwork Skills
- Accessing Scientific Information
- Designing Experimental Approaches for Studying Sugars, Amino Acids, and Glycoproteins
- Developing the Confidence to Relate Complex Organic Molecules to Biological Questions
Learning Strategies and Activities
The module will address constructivist, collaborative, active-learning styles, as well as more traditional ways of learning. We hope to strengthen student motivation by using a story line throughout the course, one which focuses on biological recognition, and also by demonstrating the relevance of the module to their lives and careers. A number of in-class activities will be developed. Our aim will be to have at least one group project as part of each class session. Laboratory projects will be investigative in nature.
Laboratory Experiments
The Glucose Pentaacetates
Papain and Benzoyl Aminoacids and/or Fumarase
Affinity Chromatography with Glycohemoglobin and Concanavilin A
We envision that the module could change student-faculty relationships in that the faculty will exercise less control in the classroom; students will have more independence and project work than is customary in organic chemistry courses. Faculty will be in the front of the classroom, in the aisles, and among students working in small groups. We hope to help students ask questions by modeling this behavior.
The module can help students think like scientists by having laboratory experiences which involve a measure of experimental design and the analysis of data. They can exercise their creativity by designing lab projects and connecting what are often seen as disparate areas of chemistry and biology. Team projects will be a part of both laboratory and classroom work. They will deal with ambiguity to some extent, and they will learn independently and collaboratively in the lab, the classroom, and outside. There will be a number of opportunities for students to communicate orally and in written form. The Internet, computer graphics, and molecular model sets will all be important molecular modeling resources for students.
Assessment of Student Learning
Students probably will have had personal experience with influenza. We can discover this and other pertinent background using a brief course questionnaire after an introduction to the module. During the course the following methods will be used and evidence assessed:
Written Exams
Interviews With Our Students
Short Papers
Student Questionnaires - Midway and End
Group Projects
Evidence of Active Learning
Class Presentations
Student Attitudes Toward the Module
Problem Set Assignments
Student Competence That is Developed
Lab Skills
Class Representatives
Oral and Written Lab Reports
Use of undergraduate laboratory assistants
Use of a student observer
problem set graders
Why should students be interested in this topic: Understanding how our cells recognize a foreign invader is an important part of perhaps the hottest current question in biology, how we process and transfer information.
Interdisciplinary aspects: Biology
Module Testing: The module will be tested at Carleton College and at Hope College. We will also attempt to have it tested at Diablo Valley College (Ron Rusay) and the University of Wisconsin (Laura Kiessling).
Learning strategies: A number of in-class activities will be developed. Our aim will be to have at least one group project as part of each class session. Laboratory projects will be investigative in nature.
Topics: How molecules recognize and bind to each other, molecular shape and polarity, intermolecular forces, the structures and stereochemistry of sugars and carbohydrates, hemiacetal and acetal formation, chemical reactions of sugars and amino acids, oligo- and polysaccharides, carbohydrates as information carriers, amino acid and protein structure, glycoproteins, viruses and cell-recognition processes.
Core concepts: The chemical principles from the current Tool Kit are structure and bonding (molecular geometry, isomers, configurations, functional groups, biopolymers), states of matter (intermolecular forces), dynamics (catalysis), reactivity (polyfunctional substances, stereochemistry, regioselectivity, and intermediates), and synthesis. The laboratory will focus on the purification, reactivity, and stereochemistry of sugars and amino acids/proteins.
Brief Description: The non-covalent binding of carbohydrates with proteins is thought to be the basis of cell recognition. In the module we will focus on the recognition of a viral protein with the sialic acid unit of a cell-surface carbohydrate. This is certainly one of the best understood systems, and influenza is something experienced by all of us, so it makes an excellent module to relate organic chemistry to our lives.
Carbohydrates are taught in most organic chemistry courses, but usually from a historical perspective that does little to suggest their important information role in biological recognition. They are probably best known to chemists for their roles in energy metabolism and as structural components of nucleic acids. Some sugars, glucose for example, serve as fuel for the immediate use of organisms through glycolysis, the citric acid cycle, and oxidative phosphorylation, whereas starch and glycogen are used for energy storage. The monosaccharides, ribose and deoxyribose, serve as part of the scaffolding of RNA and DNA.
Although carbohydrates are straightforward organic chemicals, there is complexity in their multifunctional nature and numerous stereocenters. These are often the topics which are emphasized in the organic chemistry course, with little consideration of the nifty role that carbohydrates play in the cell recognition. Although energy metabolism is an important topic, the metabolic reactions involved are the standard stuff of biochemistry, and except for consideration of a handful of examples, are best left there. However, the fundamental nature of the intermolecular forces by which biopolymers recognize and react with one another is very much organic chemistry, albeit part of the subject which is rarely considered. This is probably due to the standard structure of the two-semester organic chemistry course, which is built on the concept of treating each functional group in succession in a systematic way. It is not built around consideration of important questions which tie different classes of molecules together. An advantage of this module is that it would be used in the second semester, perhaps as a capstone, after the important functional groups have probably already been studied in the class. The module could readily be used to complement a standard organic chemistry textbook.
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