University of Kentucky s4

University of Kentucky College of Dentistry/ Education Program

Course Syllabus OBI812 DENTAL BIOCHEMISTRY (2012)

1) General Information

Director: M. Paul Murphy Starting Year/Semester: 1/1 Department: Biochemistry Ending Year/Semester: 1/1 Office: 211A Sanders-Brown COA Credit Hours: 6 Phone: 257-1412 (ext. 490) Email: [email protected] Designation: First Year #Enrolled: 57 Type: Required

Instructors: Dr. Emilia Galperin (BBSRB B169) 323-1796 [email protected]

Dr. Harry LeVine (209 Sanders-Brown COA) 257-1412 [email protected]

Dr. Kathleen O’Connor (BBSRB B369) 323-7534 [email protected]

Dr. Sabire Ozcan (BBSRB B155) 257-4821 [email protected]

Dr. Peter Zhou (BBSRB B377) 323-4474 [email protected]

Dr. Haining Zhu (BBSRB B165) 323-6052 [email protected]

2) Purpose (course/catalog description)

This is a 6 credit hour course with the objective of enriching the basic science education of dental students in the fundamental and modern principles of biochemistry. This component of the curriculum is intended to provide the biochemical background for subsequent courses in microbiology and molecular pharmacology, understanding relevant biochemical concepts when reading scientific journals during your dental career, as well as a solid preparation for the Dental Board examination. The course will be based on the excellent and "user-friendly" textbook: Biochemistry (6th Edition) by Berg, Tymoczko and Stryer (publisher-W. H.

1 Freeman and Co.). This is a terrific book, and the one that first exposed me to biochemistry as an undergraduate (although back then it was only on the 3rd edition).

3) Goals

a. College Competencies Addressed:

(#2) The new dentist must be able to acquire, analyze, and synthesize information in a scientific, critical and effective manner.

(#3) The new dentist must be able to communicate effectively, both orally and in writing, with colleagues, other health care providers, staff, patients, and the public.

(#4) The new dentist must be able to collect, record, and evaluate the biological, psychological, and social information needed to assess the patient’s oral and general health. This includes the ability to recognize and manage behavioral factors that affect oral health and utilize the information to implement strategies that facilitate the delivery of oral health care.

(#5) The new dentist must be able to establish a differential, provisional or definitive diagnosis by interpreting and correlating findings from the history, consultations, and examination.

b. Specific Goals Provide both a basic and advanced vocabulary for the future learning and understanding of the modern science of biomedicine. This includes: Learn the basics of the biological macromolecules: lipids, proteins, and nucleic acids. Learn the basics of metabolism and how it is regulated. Learn the basics of genetics and inheritance. Learn the basics of gene regulation and how it can go wrong. Learn the basics of membrane biology and signal transduction.

Although the emphasis of the course is on basic science, we also cover a range of examples (some case-based) of relevance to general medicine, dentistry and oral health: a. Disorders of protein conformation in human health, with an emphasis on transmissible prion diseases and the (controversial) possibility of transmission through contaminated dental instruments. b. How transcription and translation are perturbed in amelogenesis imperfecta, a common human genetic disorder of enamel malformation. c. Discussion of matrix metalloproteases and the balance with tissue inhibitors governing collagen breakdown in both tissue remodeling and in chronic periodontal inflammation.

2 d. Genetic mutations that cause familial tooth agenesis and predisposition to colorectal cancer (AXIN2), hereditary gingival fibromatosis type I (SOS1), e. The role of the PAX9 gene in oligodontia. f. Deletions in the FAT suppressor gene that lead to oral cancer. g. Explain how the structures of extracellular matrix macromolecules are related to their function within oral tissues, and how changes in extracellular matrix structure that occur in genetic and acquired disorders of connective tissues are related to manifestations of these diseases. h. The composition of saliva, its role in mineralization and demineralization of enamel and the types and functions of salivary proteins. i. Basic principles of human nutrition, with particular reference to the treatment and counseling of the dental patient. j. The metabolic functions of vitamins, essential fatty acids and anti-oxidants.

4) Outcomes

At the end of the course the students will have a solid understanding of the basics of biochemistry, and its relevance to dentistry and oral health. Students will have an integrated view of the role of the role of various macromolecules in biology, their function in the body, and how they can become abnormal in disease. Students will learn the basics of metabolism and nutrition, cellular signaling mechanisms, genetics and cancer, and will acquire a working vocabulary applicable to all areas of 21st century biomedicine.

5) Learning Resources

a. Required Biochemistry (6th Edition) by Berg, Tymoczko and Stryer (W. H. Freeman and Co.).

Lecture Notes: You can access the pertinent notes approximately two days prior to the scheduled lecture at http://www.uky.edu/Blackboard/, under OBI/BCH812. Some of the lectures may be posted earlier than that. Occasionally, additional material may be added by the lecturers, and you will be informed of any last minute additions or corrections.

b. Supplemental Instructors may provide material, articles, or problems associated with their lectures. These will be available for download from the course blackboard site (see above).

6) Evaluation Methods Overview

3 a. Grading Scale

A = 90 - 100% B+ = 83 - 89% B = 75 - 82% C = 60 - 74% E = < 60%

While the ranges indicated above will be the primary basis for determining the grade, adjustments may be made depending on the final distribution of exam scores.

b. Evaluation Components 4 equally weighted multiple choice exams.

c. Attendance Policy Although attendence does not influence grading, students are expected to attend all lectures. The course director should be notified in the event of any absence.

d. Late Assignments Policy N/A

e. Missed/Make-Up Exam Policy Students are required to contact the course director in advance of any planned absence in order to make arrangements to schedule a make-up exam. These must be well justifed. Examinations missed due to unplanned absences are handled on a case-by-case basis, and usually require the student to present appropriate documentation.

f. Policy for Extra Credit Work N/A

7) Policy and Procedures

a. Office Hours/Contacting Faculty Meetings with course instructors are by appointment, or during scheduled hours as indicated at the beginning of their series of lectures.

b. Changing Class Times/Exams Students will be notified as far in advance as possible if there are any changes to the syllabus. These are rare, and are coordinated with the College of Dentistry.

c. Remediation No remediation will be given prior to the awarding of the final grade, and the only option for failure (grade of E) is to retake the course once a final failing grade is turned in to the Registrar's Office.

4 d. Cheating and Plagiarism All activities in this course are conducted under the College of Dentistry’s “Code of Professional and Academic Responsibility.” It is your responsibility to review this document and be familiar with the policies and procedures contained therein. The College has high expectations of each student dentist concerning their professional and academic responsibilities including self-governance. If you have questions about expected standards of behavior, it is your responsibility to discuss and clarify these questions with the course director.

8) Instructional Sessions or Calendar Classes are from 10 am – 12 pm on each day. Note: the room is sometimes different.

Lecture / Instructor Day Date Chapter Number and Topic Room 1-Murphy W 8-Aug 1-Biochemistry: An Evolving Science MN463

2-Galperin F 10-Aug 2-Protein Composition and Structure MN463

3-Galperin T 14-Aug 3-Exploring Proteins and Proteomes MN463

4-Galperin W 15-Aug 4-DNA, RNA and the Flow of Genetic Information MN463

5-LeVine R 16-Aug 5-Exploring Genes and Genomes MN463

6-LeVine T 21-Aug 6-Exploring Evolution and Bioinformatics MN363

7-LeVine W 22-Aug 8-Enzymes: Basic Concepts and Kinetics MN363

8-LeVine R 23-Aug 7/9-Hemoglobin and Catalytic Strategies MN363

9-LeVine M 27-Aug 10-Regulatory Strategies MN363

10-O'Connor T 28-Aug 12-Lipids and Cell Membranes MN363

11-O'Connor W 29-Aug 12-Lipids and Cell Membranes MN363

Review Session R 30-Aug Review (Murphy / Galperin / LeVine) MN363

Exam I R 6-Sep Examination I on Lectures 1-9 (10 and 11 on Exam II) MN363

12-O'Connor F 7-Sep 13-Membrane Channels and Pumps MN363

13-O'Connor M 10-Sep 14-Signal-Transduction Pathways MN363

14-O'Connor T 11-Sep 14-Signal-Transduction Pathways MN363

15-Murphy F 14-Sep Introductory Human Genetics and Genomics MN363

16-Murphy T 18-Sep Genetic Diseases and Inheritance (I) MN363

5 17-Murphy W 19-Sep Genetic Diseases and Inheritance (II) MN263

18-Murphy R 20-Sep Genetics of Oral Cancers MN363

Review Session T 25-Sep Review (O'Connor / Murphy) MN363

Exam II F 28-Sep Examination II (Lectures 10-18) MN363

19-Zhou T 2-Oct 11-Carbohydrates/Proteoglycans, Mucins and Saliva MN463

20-O'Connor R 4-Oct 22-Fatty Acid Metabolism I MN363

21-O'Connor R 11-Oct 22-Fatty Acid Metabolism II MN363

22-O'Connor F 12-Oct 26-The Biosynthesis of Membrane Lipids and Steroids MN363

23-Ozcan R 18-Oct 16-Glycolysis and Gluconeogenesis I MN363

24-Ozcan F 19-Oct 16-Glycolysis and Gluconeogenesis II MN363

25-Ozcan W 24-Oct 17-Citric Acid cycle MN363

26-Ozcan R 25-Oct 18-Oxidative Phosphorylation MN563

Review Session R 1-Nov Review (Zhou / Ozcan / O'Connor *) MN363

Exam III M 5-Nov Examination III (Lectures 19-26) MN363

27-Ozcan W 7-Nov 21-Glycogen Metabolism MN263

28-Zhu F 9-Nov 23-Protein Turnover and Amino Acid Catabolism MN363

29-Zhu T 13-Nov 24-Biosynthesis of Amino Acids MN363

30-Zhu R 15-Nov 25- Nucleotide Biosynthesis MN363

31-Zhu F 16-Nov 28-DNA Replication Repair and Recombination MN363

32-Zhu M 19-Nov 29-RNA Synthesis and Processing MN363

33-Ozcan T 20-Nov 30-Protein Synthesis MN363

34-Ozcan T 27-Nov 27-Integration of Metabolism MN363

35-Ozcan R 29-Nov 31-The Control of Gene Expression MN363

Review Session M 3-Dec Review (Zhu / Ozcan) MN363

Exam IV F 7-Dec EXAMINATION IV (Lectures 27-35) MN363