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BIOCHEMISTRY 生物化学. 2011.08.30. PLEASE TURN OFF OR SILENCE YOUR PHONE. Lecturers: Wang, Fei ( 王菲 ) Ph.D College of Biotechonology Institute of Sericulture & Systems Biology Li, Guanrong ( 李关荣 ) Ph.D College of Agronomy and Biotechnology Office Hours: Tuesday, 4:00-5:30PM

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BIOCHEMISTRY

生物化学

2011.08.30

PLEASE TURN OFF OR SILENCE YOUR PHONE


Lecturers: Wang, Fei (王菲) Ph.D

College of Biotechonology

Institute of Sericulture & Systems Biology

Li, Guanrong (李关荣) Ph.D

College of Agronomy and Biotechnology

Office Hours: Tuesday, 4:00-5:30PM

Faculty’s Office (科技楼1楼)

Email: [email protected]

[email protected]


Textbooks & References

生物化学教程

王镜岩 朱圣庚 徐长法 主编

高等教育出版社

  • 生物化学(第三版)

    王镜岩 朱圣庚 徐长法 主编

    高等教育出版社

  • Lehninger Principles of Biochemistry(Fourth Edition)

    David L. Nelson Michael M. Cox

    W.H. Freeman and Company


Grading Method

  • 出勤: 20% (-7/缺席; 3次缺席= 0)

    病假或事假需要医生或班主任签字的假条

  • 平时小测验: 15%X2

    测验1安排在“核酸的结构与性质”结束后

    20-25分钟,以基本概念为主

    测验2安排在“蛋白质的降解”结束后

    对科学研究成果的介绍,以小组(6~8人/组)形式完成

  • 期终考试: 50%


What is “Biochemistry”?

Biochemistry describes in molecular terms the structures,mechanisms, and chemical processes shared byall organisms and provides organizing principles thatunderlie life in all its diverse forms, principles we referto collectively as the molecular logic of life.

生物化学在分子水平上阐述所有有机体所共有的结构、机制和化学过程,并归纳各种生命形式的组成原理(生命的分子逻辑)。


Major aspects
Major aspects

  • various types of biomolecules

    四种基本的生物大分子(蛋白质、多糖、脂质、核酸)

  • biochemical reactions, enzymes

    生化反应以及催化反应的酶等

  • bioenergetics

    生物能学

  • Metabolism, biodegradation & biosynthesis of biomolecules

    新陈代谢,生物分子的降解和合成

  • information pathway and regulation

    遗传信息的传递过程和调控


Why we study biochemistry
Why We Study Biochemistry

  • Because it is the mandatory course, we need its credits for graduation

  • Because it is the foundation of other bio-courses (cell biology, molecular biology, genetics, immunology, etc), we need to have a solid background for further studies

  • Because it is required in most graduate school entrance exams (bio-related majors), we need a high score

  • Because it is the routine questions on job interviews (bio-related), we need to answer them correctly and smartly


Why we study biochemistry1
Why We Study Biochemistry

  • Why blood type A can’t be transfused into the person with type B?

  • Why our muscle feels “sore” after an exhausting sport game?

  • Why penicillin only kills bacteria not hosts?

  • Why some silkworm larvae are transparent?

  • How silk protein changes from liquid state to solid state?

  • What other applications does silkworm have?

Because it is all about life!


How to study biochemistry
How to study Biochemistry

  • Prepare yourself with the upcoming classes

  • Come to the class and take notes

  • Understand the classical experiments and thoughts that led to the foundation of principles

  • Keep in mind certain formula, structures, conventions and reactions

  • Be aware with the degree of speculativeness on certain models

  • Find out the aspects that need further studies (your interest)


Biomolecules Are Constructed by a Variety of carbon bonding


Biomolecules Are Compounds of Carbon with a Variety of Functional Groups (官能团或功能基)


( Functional Groups 乙酰辅酶A)


Macromolecules Functional Groups Are Polymers of block-building molecules

Proteins: polymers of amino acids

Poly-saccharides: polymers of sugars

Lipids: composed by fatty acids, glycerol, choline,….

Nucleic acids: polymers of nucleotides


Organization of biomolecules
Organization of Biomolecules Functional Groups


http://multimedia.mcb.harvard.edu Functional Groups /

http://cyberbridge.mcb.harvard.edu/

http://www.openculture.com/biology_free_courses


Configuration and Conformation Functional Groups

Configuration(构型): the fixed spatial arrangement of atoms 原子在空间的排列形式

Stereoisomers(立体异构体): molecules with the same chemical bonds but different stereochemistry-different configuration 具有相同的化学键,但价健在三维空间的构型不同的分子

构型的立体化学特点在不发生共价键的断裂和重排的情况下是不会发生改变的


两种原因产生的立体异构体 Functional Groups

Geometric isomerism/cis-trans isomerism:几何/顺反异构体,由于双键或环的存在,限制了取代原子或原子基团绕键轴的自由旋转而产生的立体异构体

(顺丁烯二酸)

(反丁烯二酸)


Optical isomerism: Functional Groups 光学异构体,由于手性中心的存在,绕手性中心的取代基团以特定的顺序排列而形成的立体异构体

Chiral center (手性中心): A carbon atom with four different substituents asymmetric arranged 具有4个不同取代基团的四面体碳原子,也称为不对称碳原子或手性碳原子


A molecule with only one chiral carbon can have two stereoisomers; when two or more (n) chiral carbons are present, there can be 2nstereoisomers.

具有一个手性碳原子的分子有两个光学异构体;有多个(n)手性碳原子的分子,有2n光学异构体。


为什么称为光学异构体? stereoisomers; when two or more (

atl=[a]tlcl

c:待测液浓度 l: 偏振光通过待测液路径的长度

[a]tl比旋率


Mirror image
光学异构体的特性:互为镜像 ( stereoisomers; when two or more (mirror image)


Enantiomers ( stereoisomers; when two or more (对映体): stereoisomers are mirror images of each other 一对对映体除具有旋转程度相同而方向相反的旋光和因此导致的生物活性以外,其他物理化学性质完全相同

Diastereomers (非对映体): pairs ofstereoisomers that are not mirror images of each other 往往存在于有多个手性中心的分子间,物化性质也不同


立体异构体的命名和表述方式 stereoisomers; when two or more (

  • DL体系:单糖和氨基酸根据甘油醛的绝对构型命名,和旋光方向无关


  • RS stereoisomers; when two or more (系统

  • 手性碳上4个取代基的优先顺序:

  • 使优先性最小的取代基离开观察者最远,另三个取代基面向观察者

  • 确定靠近观察者的三个取代基的优先顺序,顺序是顺时针方向的,为R(right)构型,反之为S(left)构型


Racemate d l stereo specificity
外消旋物( stereoisomers; when two or more (racemate):以D、L两种手性形式等摩尔混合物存在的化合物,不能使偏振光发生旋转立体专一性(stereo-specificity):区分立体异构体的能力,是酶和其他蛋白质的一种特性


Conformation stereoisomers; when two or more ((空间构象): the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds

由于分子中单键自由旋转以及键角有一定柔性,具有同一结构式和同一构型的分子在空间上以多种形态存在,且各种形态之间的变换不需要任何共价键的断裂和重排


三种分子模型 stereoisomers; when two or more (

  • 骨架式

  • 球棍式

  • 空间填充式


分子间的非共价相互作用 stereoisomers; when two or more (

  • Electrostatic interaction (静电相互作用,盐桥)

    带电荷的基团之间的相互作用

  • Hydrogen bond (氢键)

    偶极矩引起的氢核裸露,和另一电负性大的原子产生的静电吸引力

  • van der Waals force (范德华氏力)

    弱静电相互作用:偶极与诱导偶极,瞬时偶极和诱导偶极间


23kJ/mol

470kJ/mol


液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)


Water forms hydrogen bonds with polar solutes液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)


  • 亲水化合物(液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)hydrophilic)


  • 疏水化合物(液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)hydrophobic)

Hydrophobic interaction:

The forces that hold the nonpolar regions of the molecules together


  • 两亲化合物(液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)amphipathic)


Molecular Weight, Molecular Mass, and Their Correct Units液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)

Mr: molecular weight (relative molecular mass)

is defined as the ratio of the mass of a molecule of that substance to one-twelfth the mass of carbon-12 (12C)

一个分子质量与一个12C原子质量的1/12的比值,没有单位

Molecular mass (m):mass of one molecule, or the mo-

lar mass divided by Avogadro’s number

分子质量,单位“道尔顿”,dalton,缩写为d或Da

1 d= 12C原子质量的1/12,即 1.6602x10-27kg

1nm=10Å=10-3mm=10-6mm=10-9m

1pg=10-3ng=10-6mg=10-9mg=10-12g


Chemical evolution of biomolecules
Chemical Evolution of Biomolecules液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)


基本构件分子液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)

  • 20种氨基酸

  • 5种碱基

  • 2种单糖

  • 1种醇

  • 1种脂肪酸

  • 1种胺


Wish we all have a good journey in biochemistry
Wish we all have a good journey in Biochemistry液态水的氢键平均寿命短暂,导致液态水的结构是一种时间和空间上的统计结构,既是流动的(氢键破裂时)又是固定的(氢键形成时)


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