Course Title: BiochemistryCredit units: 4Instructors: All members of faculty from Department of Biochemistry

Biochemistry can be defined as the science concerned with the chemical basis of life. Since cell is the structural unit of living systems, a functional definition of biochemistry can be:” the science concerning with the chemical constituents of living cells and with the reactions and processes that they undergo”.

Course Description:This course seeks to describe the structure, organization, and fun

ctions of living matter in molecular terms. Three principal areas will be covered: (1) the structural chemistry of the components of living matter and the relationship of biological function to chemical structure, (2) metabolism, the chemical reactions that occurs in living matter, and (3) molecular genetics which provides introduction on how genetic material is replicated, recombined and maintained, how the genetic information is flowed from DNA to protein, and how these processes are regulated. The different subjects covered in this course will be taught by different members of faculty whose research interest is in line with the covered subject. This course is offered as an introductory course of biochemistry and is intended for undergraduate students.

Textbook: Lehninger’s “Principles of Biochemistry”, 5th edition, 2008Reference: Marks’ “Basic Medical Biochemistry, A Clinical Approach”, 2nd

edition, 2005. Lange’s “Case FilesTM: Biochemistry”, 2nd edition, 2008

2/21 1. Introduction (1-2) 王子堅2/23 2. Amino Acids, Peptides, and Proteins (3) （ I ） 游佳融※2/28 3. The Three Dimensional Structure of Proteins （ I ） (4) 游佳融3/01 4. The Three Dimensional Structure of Proteins （ II ） (4) 游佳融3/06 5. Protein Function (5) 余兆松3/08 6. Enzymes (I) (6) 余兆松3/13 7. Enzymes (II) (6) 余兆松3/15 8. Principles of Bioenergetics (13) 鄭邑荃3/20 9. Carbohydrates and Glycobiology (I) (7) 吳明道3/22 10. Carbohydrates and Glycobiology (II) (7) 吳明道

4/02~4/06 First Examination (20%) 游佳融 / 余兆松 / 吳明道 / 鄭邑荃

3/27 11. Nucleotides and Nucleic Acids (8) 林光輝3/29 12. Lipids (10) 林光輝

4/03 13. Biological Membrane and Transport （ I ） (11) 林光輝4/05 14. Biological Membrane and Transport （ II ） (11) 林光輝4/10 15. Glycolysis and the Catabolism of Hexoses (14,15) 洪錦堂4/12 16. The Citric Acid Cycle (16) 洪錦堂4/17 17. Oxidative Phosphorylation (19) 洪錦堂4/19 18. Carbohydrate Biosynthesis (20) 洪錦堂

4/30~5/04 Second Examination (20%) 洪錦堂 / 林光輝

課程代號 :MD2010 Biochemistry (School year 2011) School of Medicine　 Date Topics (Chapters) Instructor

4/24 19. Fatty Acid Catabolism (17) 白麗美4/26 20. Lipid Biosynthesis （ I ） (21) 白麗美5/01 21. Lipid Biosynthesis （ II ） (21) 白麗美5/03 22. Amino Acid Catabolism (18) 簡昆鎰5/08 23. Biosynthesis of Amino Acids and Nucleotides (22) 簡昆鎰5/10 24. Integration of Metabolism （ I ） (23) 簡昆鎰5/15 25. Integration of Metabolism （ II ） (23) 簡昆鎰

5/21~5/25 Third Examination (20%) 白麗美 / 簡昆鎰5/17 26. Genes and Chromosomes (24) 王子堅5/22 27. DNA Metabolism (I) (25) 王子堅5/24 28. DNA Metabolism (II) (25) 王子堅5/29 29. RNA Metabolism (26) 柯博元5/31 30. Protein Metabolism (27) 柯博元6/05 31. Regulation of Gene Expression (28) 柯博元6/07 32. DNA-Based Information Technologies (9) 吳嘉霖6/12 33. Biosignaling （ I ） (12) 游佳融6/14 34. Biosignaling （ II ） (12) 游佳融

6/18~6/22 Final Examination (20%) 王子堅 / 趙清貴 / 游佳融

*Grades are determined by four examinations (80%) and “Take-home” exams (20%)

*2 月 28 日為和平紀念日，請生化小老師調查同學選課狀況後，與游佳融老師討論調課事宜，時間確定後請自行向教務處借用教室，並通知老師上課地點

Biochemistry Laboratory and clinical correlation (school year 2011)School of Medicine

Date Topics Instructors

※2/24/(13:10-17:00) 1. Check-in/Basic techniques 王子堅 /洪錦堂＊ 3/09/(13:10-17:00) 2. Enzyme reaction /Determination of proteins 簡昆鎰 /吳嘉霖＊ 3/23/(13:10-17:00) 3. Blood specimen preparation; glucose analysis 吳明道 /洪錦堂

; neutral sugar determination; sialic acid assay ＊ 4/06/(13:10-17:00) 4. Serum proteins/serum lipids 游佳融 /白麗美＊ 4/20/(13:10-17:00) 5. Liver function test; renal function test 王子堅 /鄭邑荃 5/04/(13:10-17:00) 6. Amplification of HBx in serum by PCR 趙清貴 /鄭邑荃＊ 5/18/(13:10-17:00) 7. DNA quantitation and DNA mapping 林光輝 /趙清貴＊ 6/01/(13:10-17:00) 8. ELISA for HbsAg and α-FP 余兆松 /白麗美

6/15/(11:10-12:00) 9. Final Examination/ Check-out 王子堅 /簡昆鎰

Part B Clinical correlation3/09 (10:10-12:00) Student/teacher discussion (1) 生化暨分生科 6 位老師參加3/23 (10:10-12:00) Student/teacher discussion (2) 生化暨分生科 6 位老師參加4/06 (10:10-12:00) Student/teacher discussion (3) 生化暨分生科 6 位老師參加4/20 (10:10-12:00) Student/teacher discussion (4) 生化暨分生科 6 位老師參加5/18 (10:10-12:00) Student/teacher discussion (5) 生化暨分生科 6 位老師參加6/01 (10:10-12:00) Student/teacher discussion (6) 生化暨分生科 6 位老師參加

6/15 (13:10-17:00) Student presentation 生化暨分生科 10 位老師參加

Clinical correlation (PBL) 學生需知1. 請準時 10:10--12:00 ( 評分重要依據之一， 10:30 以後即為缺席，遲到依時間每 5 分鐘扣 20%)2. 請注意一般禮儀 PBL 主要目的之一是為培養同學參與專業人員討論之能力 (EQ 與 IQ 同樣重要 ) 請

儘量表達您的意見，但也請尊重同學發言的機會。3. 請依拿到的 problem 就各種描述的情況，對該 case 列出他 ( 或她 ) 的問題 --- 不要

作診斷，只要列出問題。當然過程中可以就病情作猜測，發表你的看法 or postulates ，但重點是實事求是，先釐清現象，列出所有的數據 (data) 。

4. 請儘量討論各項情況並開始列出 learning issues— 由研判症狀對各項不清楚的生化原理列出應該自行研究的課題，對已知的範圍也請討論。

5. 下課後請先就各 learning issues 在參考書中找相關資料，如果時間許可，請再從知名學報 ( 如 New England Journal of Medicine , Nature , Science , Lancet , Journal of Clinical Investigation , 及各 Review 性質的學報 ) 作進一步的研究。

6. 第二次上課時，請將整理過的資料 ( 附出處 ) 說明意義與已知情況的關係，每一位同學均應有整體的準備，互相補充，解釋各種可能。如還有不清楚的地方，再增列 learning issues 。

7. 第三次上課 (PBL--wrap up) 前儘可能對相關資料整理清楚，如仍有不明白處，可在wrap-up 時發問。

8. Tutors 會儘量避免說明任何與內容有的的資訊。 PBL 的另一個重點是學習過程，答案正確性並不是最重要的目的，亦即經由從問題 ( 現象 ) 開始，發掘自己不懂的方面 (Learning Issues) ，自行研讀，整理組織並發表，互相討論，逐步接近一個整體的了解。

9. PBL 的目的是就臨床問題導引至基礎理論與知識，最終推測的結果 ( 那一種病 ) 並非最重要，重點是經由試圖解決問題，了解自己不明白的東西。

Biochemistry is a Science Dealing with the

Chemistry of Living Matter• We know quite well what is chemistry• But what is living matter?

Life is characterized by• High degree of complexity• Extraction, transformation, and systematic use of energy

to create and maintain structures and to do work• Ability to sense and respond to changes in surrounding• A capacity for fairly precise self-replication while allowing

enough change for evolution

Life is Complex

• Living organisms have– internal structures with defined functions– large number of different compounds– macromolecules that are capable of highly sp

ecific interactions

Six Kingdoms of Life

Six kingdoms

• Archaea• Bacteria• Protista• Fungi• Plantae• Animalia

Living things are placed in kingdoms on the basis of similarities and differences at the organism, cellular, and molecular levels

Cellular organization

Unicellular prokaryoteUnicellular prokaryoteUnicellular eukaryoteUni- or Multicellular eukaryoteMulticellular eukaryoteMulticellular eukaryote

Cell: The Universal Building Block • Living organisms are made of cells• Simplest living organisms are singe-celled• Larger organisms consists many cells with

different functions• Not all the cells are the same

Bacterial, Plant, and Animal Cells are Different

• The internal structure and properties of cells from organisms in different kingdoms are rather different

Structure Composition Function

Cell wall Peptidoglycan Mechanical support

Cell membrane Lipid + protein Permeability barrier

Nucleoid DNA + protein Genetic information

Ribosomes RNA + protein Protein synthesis

Pili Protein Adhesion, conjugation

Flagella Protein Motility

Cytoplasm Aqueous solution Site of metabolism

Components of Bacterial Cell

Eukaryote Cells: More Complexity• Have nucleus by definition

– protection for DNA; site of DNA metabolism– selective import and export via nuclear membrane pores– some cells become anuclear (red blood cells)

• Have membrane-enclosed organelles– Mitochondria for energy in animals, plants and fungi– Chloroplasts for energy in plant– Lysosome for digestion of un-needed molecules

• Spatial separation of energy-yielding and energy consuming reactions helps cells to maintain homeostasis.

Cytoplasm and Cytoskeleton

• Cytoplasm is highly viscous solution where many reactions take place

• Cytoskeleton consists of microtubules, actin filaments, and intermediate filaments– cell shape– transport paths– movement

The three types of cytoskeletal filaments

Chemical Foundations

• The four most abundant elements in living organisms are H, O, N, and C.

• Elements H, O, N, P, S are also common• Metal ions (e.g. K+, Na+, Ca++, Mg++, Zn++, Fe++)

play important roles in metabolism• Together, about 30 elements are essential for

life

Biomolecules

Biomolecules are compounds of carbon with a variety of functional groups

• Cells contain a universal set of small molecules which include common amino acids, nucleotides, sugars and their phosphorylated derivatives, and mono-, di-, and tricarboxylic acids.

• Macromolecules are the major constituents of cells. The four major macromolecules are proteins, nucleic acids, polysaccharides and lipids.

• Three-dimensional structure is described by configuration and conformation. Stereoisomers and optical isomers have different biological properties.

• Interactions between biomolecules are specific. Macromolecules have unique binding pockets. Only certain molecules fit in well and can bind.