Biochemistry 生物化学

For Class of Spring, 2004 Office: Linhong Low, Room 502

Instructor: Yicheng CaoPhone No: 87111474; Email: yccao@scut.edu.cn

Outline of the class• Textbook: Biochemistry:An Introduction(second Edition), 中国科学院研究生教学

丛书－－生物化学导论（第二版）， Ed. by Trudy McKee & James McKee, 科学出版社 & MiGraw-Hill Companies, Inc., 2001

Reference Book: Molecular Biology (second Edition), 中国科学院研究生教学丛书－－分子生物学

（第二版）， Ed. by Robert F.Weaver, 科学出版社 & MiGraw-Hill Companies, Inc., 2002

Instant Notes in Biochemistry, 现代生物学精要速览－－生物化学， Ed. by B.D.Hames et all, 科学出版社＆ Bios Scientific Publishers Limited, 2002

生物化学，王镜岩等，第三版，高等教育出版社，２００２• Schedules : Wednesday Afternoon in Weeks 1-19 Friday Morning in Weeks 2,4,…18 • Scoring: Attendance 10% Homework 30% Examination 60% (mid-term or final-term exam if needed)

• Basic concepts of biochemistry• Biochemistry as a chemical science• Distinction between inanimate matter from

living organisms• Biological molecules or biomolecules• Biochemistry as an interdisciplinary science• Dynamic cells• Basic methods in biochemistry• Biochemistry in application

Introduction to Biochemistry

Roots of Biochemistry

• The present day biochemistry is the interweaving product of historical traditions of biochemistry, cell biology, and genetics.

Friedrich Wohler’s successful synthesis of urea from ammonium cyanate (1828)

• Roots of biochemistry (cont’d)

•  Hans Buchner and Eduard Buchner’s discovery of in vitro fermentation in 1897, quite by accident. They were interested in manufacturing cell-free yeast extract for possible therapeutic use. These extracts had to be preserved without anticeptics such as phenol, and so they decided to try sucrose, a commonly used preservative in kitchen chemistry. They obtained a startling result: sucrose was rapidly fermented into alcohol by the yeast juice. The significance of this finding is that they demonstrated for the first time fermentation could occur outside the cell. This was in contrast to the accepted view of their day, as asserted by Louis Pasteur, that fermentation was inextricably tied to living cells. The chance discovery opened up modern biochemistry. Metabolism became chemistry.

• Crystallization of urease by JB Sumner in 1925

 • Cell Biology: Robert Hook’s observation of cells

(1600’s); Walter Flemming’s discovery of chromosomes (1875), identified as genetic material (1902)

• Genetics: Gregor Mendel’s suggestion of gene as the unit of heredity (1800’s); Hershy and Chase’s demonstration of DNA as the genetic material (1950’s); Watson/Crick’s double helix (1953)

Questions asked by biochemists

• What are the chemical structures of the components of living matter?

• How do the interactions of these components give rise to organized supramolecular structures, cells, multicellular tissues, and organisms?

• How does living matter extract energy from its surroundings in order to remain alive?

Questions asked by biochemists (cont’d)

• How does an organism store and transmit the information it needs to grow and to reproduce itself accurately?

• What chemical changes accompany the reproduction, aging, and death of cells and organisms?

• How are chemical reactions controlled inside living cells?

• The search for the answers is the study of the chemistry of life.

1. The structural chemistry of the components of living matter and the relationship of biological function to chemical structure.

2. Metabolism - the totality of chemical reactions that occur in living matter.

3. The chemistry of processes and substances that store and transmit biological information (molecular genetics).

Three major areas (cont’d)

Biochemistry as an multidisciplinary science

It can be divided into three principal areas:

1. The structural chemistry

2. Metabolism

3. Molecular genetics

Biochemistry draws its major themes

From:

1. Organic chemistry 5.Microbiology

2. Biophysics 6. Physiology

3. Medical research 7. Cell biology

4. Nutrition 8. Genetics

The major themes

1. Organic chemistry, which describes the properties of biomolecules;

2. Biophysics, which applies the techniques of physics to study the structures of biomolecules;

3. Medical research, which increasingly seeks to understand disease states in molecular terms;

4. Nutrition, which has illuminated metabolism by describing the dietary requirements for maintenance of health;

The major themes (cont’d)

5. Microbiology, which has shown that single-celled organisms and viruses are ideally suited for studying many metabolic pathways and regulatory mechanisms;

6. Physiology, which investigates life processes at the tissue and organism levels;

7. Cell biology, which describes the biochemical division of labor and life processes within a cell;

8. Genetics, which describes mechanisms that give a particular cell or organism its biochemical identity.

What distinguishes living organisms from inanimate matter?

• Living organisms are composed of lifeless molecules, which conform to all the physical and chemical laws that describe the behavior of inanimate matter. Yet living organisms possess extraordinary attributes not exhibited by any random collection of molecules. Biological chemistry is to study the properties of biomolecules that distinguish them from other collections of matter, and then identify the principles that characterize all living organisms.

What distinguishes living organisms from inanimate objects (cont’d)

• 2. Living organisms extract, transform, and use energy from their environment. The energy enables them to build and maintain their intricate structure or to do work.

In contrast, inanimate matter does not absorb energy to do work; rather, it tends to decay towards a more disordered state, and reaches equilibrium with its surroundings.

What distinguishes living organisms from inanimate objects (cont’d)

• Living organisms are not at equilibrium with their surroundings.

• They use energy to concentrate ions from their surroundings, for example.

--The absorption of ions is an active process and consumes energy.

Essence of life: “Life is for life”

• Each component of a living organism has a specific function. This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures such as the nucleus or chloroplast and of individual chemical compounds. The interplay among the chemical components of a living organism is dynamic; changes in one component cause coordinating or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual constituents. The collection of molecules carries out a program, the end result of which is reproduction of the program and self-perpetuation of that collection of molecules; in short, life.--Lehninger

What distinguishes living organisms from inanimate objects (cont’d)

• 3. The capacity for precise self-replication and self-assembly—the quintessence of the living state.

--Billions of daughter cells can carry a faithful copy of the genetic material of their parental cell. This replication is not quite like what Schrodinger believed in his “What Is Life”.

Ecosphere

Population

Hierorchical Organization of Multicellular Organisms

Individual

Organ System

Organ

Tissue

Cell

Organelle

Molecule

Cell Organization

• Prokaryote: Cell wall, Plasma membrane, Mesosome, (Outer membrane), (Flagellum); Cytosol; Nucleoid;

• Eukaryote: (Cell wall); Plasma membrane; Cytosol; Mitochondrion; Golgi; (Lysosome, Chloroplast); Peroxisome; (Vacuole); (Secretory vesicles); Smooth endoplasmic reticulum; Rough endoplasmic reticulum; Nucleus; Nucleolus

A mammalian cell

A plant cell

Electron micrograph of the nucleus of the alga chlamydomonas

Nucleus and nucleolus

Endomembrane system

Endoplasmic reticulum

Golgi apparatus

Lysosomes for protein degradation

Mitochondrion

Vacuoles

Cell-surface receptors or channels

Secretory cell of the pancreas, extensive endoplasmic recticulum for synthesis of protein

Portion of a skeletal muscle cell, highly organized actin and myosin filament

Collenchyma cell of plant stem

Human sperm cell, long flagella

Mature man erythrocytes, no nucleus or endomembrane system

Human embryo at the 2-cell stage

Electron micrograph showing yellow mosaic virus,tobacco mosaic virus and bacteriophage

Human immuno-deficiency virus

Molecular surface model of filamentous phage fd

Molecular surface model of the canine parvovirus

Molecular surface model of human poliovirus

Molecular surface model of the bacteriophage x174

Dynamic cell 1:Cell Cycle

protein

DNA membrane

UV

Normal cell Apoptotic cell

Apoptotic body

stimuli

Dynamic Cell 2: Programmed Cell Death

I. Nucleic acids participate in information storage, transmission, and expression.

II. Polysaccharides serve both as structural components and as reserves of biological energy.

III. Proteins - 1. perform structural roles in the body; 2. act as transport substances (e.g. hemoglobin); 3. defend an organism against infection (antibodies); 4. function as enzymes, catalyzing the thousands of chemical reactions that occur within an individual cell.

IV. Lipids serve as the major structural element of the biological membranes. They also are the major energy storage form of cells.

Biological Molecules

Diversity in biomolecules

Numerous different biomolecules in a cell

Biochemistry in application

• Disease diagnosis

• Medicine

• Drug design

• Nutrient supplements

• Research reagents

Concluding remarks

• Biochemistry is a biological science on biomolecules. In other words, the aim of biochemistry is to understand life in molecular terms.

• Biochemistry is a multidisciplinary science.• Again, life is for life.• Cell—basic unit of life: highly organized an

d dynamic.