1. Dental Biochemistry 2015 Lecture 1 Dr. Kumar, MSB E-639, x-4750 E-mail:kumarsu@njms.rutgers.edu Web site: http://njms2.umdnj.edu/biochweb/education/bioweb/ 11

2. Dental Biochemistry Examinations: There will be three unit examinations and a final comprehensive examination. Students must sign in and sign out before leaving the examination room. Grading policy is described in the handout. Any student who is late by more than 30 min will not be given the examination. If a student can not take a unit examination due to unavoidable circumstances, the student may be re- examined. A student discovered cheating on the examinations is subject to disciplinary action by the dental school. The course director will try to get tutorial help for students in academic difficulty following first unit exam. Please see the course director if you need assistance. 21

3. An all class session is held to review each examination at which time student concerns about individual questions are addressed. Individual students may challenge one or more questions through the class representative. PBL: There are three problem based learning sessions of two hours each. Attendance at these sessions is mandatory. Textbook: Lippincott’s Illustrated Reviews in Biochemistry, Lippincott Williams and Wilkins; 6 th North American Edition. ISBN-13: 978-1451175622 RECOMMENDED TEXT(s): Medical Biochemistry by Gerhard Meisenberg and William Simmons, Elsevier Publishers, 3 rd Edition Students may consult other books for content and/or explanations 31

4. GRADING POLICY Grades in the course will be based on three unit examinations and a final comprehensive examination. Each unit exam will constitute 21% of the grade. The final exam will constitute 32% of the grade. Final grades will be adjusted to give a class mean average of not less than 79. There will be three PBL sessions of 2 hours each. Five percent of the overall grade will be given to a student based on his/her performance in PBL sessions as assessed by the instructor. Attendance at PBL sessions is compulsory. Students will lose additional 1.0% of the grade for every missed PBL session. PBL session grades will be disclosed after all the PBL sessions are completed. Requests for correction or re ‑ evaluation of graded examinations must be presented to Dr. Kumar, the Course Director, within three (3) working days after the examination key has been posted. All requests must be typed. 41

5. Final Grades Letter grades will be assigned on the following basis: 89.5 and aboveA 84.5 -- 89.49B+ 79.5 – 84.49B 74.5 – 79.49C+ 69.5 – 74.49C 65-69.49 D <65F 51

6. The components of an idealized eukaryotic cell. A cell such as this probably does not exist, but the diagram shows the relative sizes and locations of the cell parts 61

7. Anabolism and Catabolism Anabolism is the phase of intermediary metabolism that encompasses the biosynthetic and energy requiring reactions. The cellular synthesis of complex substances and macromolecules from low molecular weight precursors. In general, the reactions of anabolic pathways are reductive and consume reducing potential (energy) (ATP) Catabolism refers to reactions that are energy producing, are oxidative and produce reducing cofactors (NADH, NADPH etc) 71

8. High [NADH] is indirectly equivalent to high[ATP]. This means that the cell is high in “energy”. High [NAD + ] or [ADP or AMP] means that the cell is low in “energy”. ATP + ½ ADP Energy Charge= ATP + ADP +AMP The energy charge can have a value of 0 (all AMP) to 1 (all ATP). Regulation of the degradation and synthesis depends on the energy state of the cell (ATP) 81

9. Synthetic and degradative pathways are distinct. Synthesis Degradation If [ATP] is low, degradative pathways are stimulated. If [ATP] is high, degradative pathways are inhibited and synthetic pathways are stimulated 91

10. Energy Charge Fluctuations The energy charge can have a value ranging from 0 (all AMP) to 1(all ATP). It has been shown that ATP-generating (catabolic) pathways are inhibited by a high energy charge. In plots of the reaction rates of such pathways versus the energy charge, the curves are steep near an energy charge of 0.9, where they usually intersect. It is evident that control of these pathways has evolved to maintain the energy charge within rather narrow limits. In other words the energy charge like the pH of a cell is buffered. The energy charge of most cells range from 0.8 to 0.95." A high Energy Charge signals the down regulation of metabolism. A low Energy Charge signals up regulation of metabolism 101

11. 111

12. 121

13. 131

14. A few reaction types are repeatedly observed in biochemistry 141

15. Oxidation-reduction Succinate DH Malate DH 151

16. Ligation Formation of carbon-carbon bond. Pyruvate carboxylase 161

17. Isomerization Aconitase 171

18. Group transfer Hexokinase 181

19. Hydrolytic reactions Peptidases 191

20. Lyases a lyase is an enzyme that catalyzes the breaking (an "elimination" reaction) of various chemical bonds by means other than hydrolysis (a "substitution" reaction) and oxidation, often forming a new double bond or a new ring structure. 201

21. Dehydration Removal of H 2 O (group) to form a double bond Enolase 211

22. Learning objectives lecture 1 Know general structure of eukaryotic cell and general functions of various structures. Know about the energy charge of a cell and conditions under which it will go up or down. Does the energy charge always stay constant? Understand general type of reactions observed in biochemistry. 221