1. Welcome to Biochemistry 432/832 Instructors: Vadim Gladyshev Lori Allison Teaching Assistant: Yun Jeong Kim yjkim@unlserve.unl.edu Class web page : http://www- class.unl.edu/bioc432/bioc432.htm Tuesday/Thursday 11.00-12.15 pm Beadle Center Auditorium

2. Outline Information Syllabus Student profile Introduction to the course Introduction to metabolism Overview of glycolysis

3. Useful web sites THE LITERATURE OF BIOCHEMISTRY http://www-class.unl.edu/bioc839/literature.html THE FIELD OF BIOCHEMISTRY Major Journals Major Reviews YOUR OWN FIELD OF RESEARCH REVIEWS KEY WORD SEARCH WHERE TO SEARCH? How to Read a Research Article Composition of a full paper Composition of a communication What to read? Skepticism

4. Useful web sites National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov Access to the primary literature (Pubmed) http://www.ncbi.nlm.nih.gov/PubMed/ http://www.ncbi.nlm.nih.gov/PubMed/ On-line journalsJ. of Biol. Chemistryhttp://www.jbc.org/http://www.jbc.org/ Proc. of the Nat. Acad of Sci. USAhttp://www.pnas.org/http://www.pnas.org/ Sequences (Entrez) http://www.ncbi.nlm.nih.gov/Entrez/ http://www.ncbi.nlm.nih.gov/Entrez/ Structures (Structure) http://www.ncbi.nlm.nih.gov/Structure/ Clusters of orthologous groups (COS)http://www.ncbi.nlm.nih.gov/COG/http://www.ncbi.nlm.nih.gov/COG/

5. Information You are welcome to come without an appointment, but it is better to E-mail or call before you come You are responsible for all material covered in the chapter that is discussed in the class. You will have the reading assignment for each class period except exams. Some sections of certain chapters may be excluded from the reading assignments and exams, and if it happens, I will tell you beforehand. No excuses for missing exams. Medical school interview is not an excuse.

6. Information Recent scientific papers that describe discoveries or breakthroughs in areas being covered during the course, will be discussed and corresponding concept questions may be included in the exams and bonus questions. Methods to study: read the chapter (reading assignment) before the respective class period. First, you could read quickly the chapter to get an idea what is it about. The second time you read, pay a particular attention to concepts, but knowledge of details may also be necessary. After the class, read the chapter again and also read the lecture notes. It should be enough for a good performance on exams.

7. Overview of Metabolism

8. Metabolism - Overview Metabolism is a sum of chemical changes that convert nutrients into energy and finally to complex finished products of cells (The process through which organisms acquire and utilize energy for their function) Do we know all metabolic pathways?

9. Metabolism - Overview Metabolism consists of catabolism and anabolism Catabolism: degradative pathways Usually energy-yielding! Anabolism: biosynthetic pathways energy-requiring!

10. Metabolism - Overview

11. Degradation: biomolecules – building blocks – common intermediates - final products

12. Metabolism - Overview Principles: Metabolic pathways are irreversible (because they must be regulated) Metabolic pathways have (first) committed step Metabolic pathways are regulated Metabolic pathways are compartmentalized

13. Principles: anabolic and catabolic pathways must differ in at least one step in order to be regulated Anabolic & catabolic pathways involving the same product are not the same Some steps may be common Others must be different- to ensure that each pathway is spontaneous This also allows regulation mechanisms to turn one pathway and the other off

14. Principles: Metabolic pathways are compartmentalized Mitochondria (TCA cycle, OxPhos, fatty acid oxidation, amino acid breakdown) Cytosol (glycolysis, fatty acid biosynthesis, pentose phosphate cycle) Nucleus (DNA replication, transcription, RNA processing) ER (Rough ER: synthesis of membrane and secretory proteins, smooth ER: lipid and steroid biosynthesis) Golgi (posttranslational processing of proteins)

15. Pathways consist of sequential steps - The enzymes may be separate - Or may form a multienzyme complex - Or may be a membrane-bound system - New research indicates that multienzyme complexes are more common than once thought

16. Metabolism - Overview Understanding of pathways: Sequence of reactions Mechanisms of each reaction Regulation of pathways Hypotheses or exploration ??? Methods: Inhibitors (accumulation of intermediates) Genetic defects (also accumulation of intermediates) Genetic manipulations: animals (transgenic, knockout), expression in certain tissues Emerging methods: sequence methods (genome projects), bioinformatics, high throughput gene expression methods (microarray analyses - hybridizations on membranes, slides, chips)

17. Systems Analysis of Metabolism Catabolic and anabolic pathways, occurring simultaneously, must act as a regulated, orderly, responsive whole catabolism, anabolism and macromolecular synthesis Just a few intermediates connect major systems - sugar- phosphates,  -keto acids, CoA derivatives, and PEP ATP & NADPH couple catabolism & anabolism Phototrophs also have photosynthesis and CO 2 fixation systems

18. Intermediary metabolism

19. Cells need a constant supply of energy NADH, NADPH and ATP ATP - energy currency NADPH - reducing power Glucose --> NADH --> ATP Glucose --> NADPH --> biosynthesis (reductive) Metabolism - energy considerations

20. Redox in Metabolism NAD + collects electrons released in catabolism Catabolism is oxidative - substrates lose reducing equivalents Anabolism is reductive - NADPH provides the reducing power (electrons) for anabolic processes NAD + /NADH ratio: 725Concentration: 0.5 mM NADP + /NADPH ratio: 0.015Concentration: 0.2 mM