1998: Ph.D. Nagoya University, Japan 1999-2001: Assistant Professor Aichi Medical, Japan 2001-2007:...

1998: Ph.D. Nagoya University, Japan1999-2001: Assistant Professor Aichi Medical, Japan2001-2007: Research fellow, National Institutes of Health, USA 2007-now: Professor Zhejiang University

Wei Liu （刘 伟）Tel ： 88208357

E-mail: liuwei666@zju.edu.cn

Trends in Cell Biology 2006Journal of Cell Biology 2005Nature Structural & Molecular Biology 2005Nature 2003Cell Death & Differentiation 2003

Selective publications

Autophagy 2013Journal of Cell Science 2013Hepatology 2012Journal of Cell Science 2012Journal of Hepatology 2011

Research InterestsOur laboratory is centered on the elucidation of molecular mechanisms underlying the endomembrane structures and functions by use of con-focal microscopy and analyzing protein dynamics in living cells. We are also interested in the roles of intracellular organelles involved in physiological and pathological processes such as mitosis, autophagy, aging and liver cancer development.

Endoplasmic Reticulum Golgi apparatus(red) Mitochondria Peroxosome(green)

细胞器生物学实验室Laboratory of Organelle Biology

Biochemistry

Teaching staff

IntroductionBio-molecules

Wei Liu

Enzymes

Jin-Biao Zhan Li-Hong Xu

Metabolism

Yong-Gang Chen

HormonesDNA replicationGene expression

What Is Biochemistry?

• Biochemistry studies living systems to discover and understand their chemical composition and how organisms carry out life processes.

• Combines biology and organic, inorganic or physical chemistry to study life processes.

Overview of Biochemistry Overview of Biochemistry

Brief history of Biochemistry• Originated at the end of 18th Century.

• Developed in 19th Century.

• At the beginning of 20th century, biochemistry

became an independent science.

• It was called physiological chemistry.

• From 1903, it became Biochemistry.

What is Life Made of?

• Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation.

• All students of life must have a fundamental understanding of organic chemistry and biochemistry.

Organic Chemistry

• Organic chemistry is the study of Carbon compounds.

• Organic compounds are compounds composed primarily of a Carbon skeleton.

• All living things are composed of organic compounds.

Organic Chemistry

Organic Chemistry

Carbon can covalently bond with up to four other atoms.

Carbon can form immensely diverse compounds, from simple to complex.

Methane with 1 Carbon atom DNA with tens of billions of Carbon atoms

Biochemistry

• Biochemistry is a special branch of organic chemistry that deals with matter inside the living cell called Protoplasm.

• Protoplasm is an enormously complex mixture of organic compounds where high levels of chemical activity occur.

Biochemistry

2. You will be expected to learn the basic biochemical processes of major cell functions, such as protein synthesis.

• How much biochemistry do you need to know for this course?

1. You need to know the structure of organic molecules important to major biological processes.

Primary Organic Compounds

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids

You are expected to learn the structure and functions of these organic compounds:

Polymers ands Monomers

• Each of these types of molecules are polymers that are assembled from single units called monomers.

• Each type of macromolecule is an assemblage of a different type of monomer.

Monomers

Macromolecule

Carbohydrates

Lipids

Proteins

Nucleic acids

Monomer

Monosaccharide

Not always polymers

Amino acids

Nucleotides

How do monomers form polymers?

• In condensation reactions (also called dehydration synthesis), a molecule of water is removed from two monomers as they are connected together.

Hydrolysis

• In a reaction opposite to condensation, a water molecule can be added (along with the use of an enzyme) to split a polymer in two.

Four major classes of biomolecules

· Carbohydrate

· Proteins

· Nucleic acid

· Lipids

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds

with multiple hydroxyl groups.

Sugar: (C-H2O)n

Aldehyde: -CHO

Ketone: C=O

Hydroxyl: -OH

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups.

Function:

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups.

Function: (1) serves as energy stores, fuel, and metabolic intermediates.

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups.

Function: (1) serves as energy stores, fuel, and metabolic intermediates.

(2) ribose and deoxyribose sugars form part of the structure framework of RNA and DNA.

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups.

Function: (1) serves as energy stores, fuel, and metabolic intermediates.

(2) ribose and deoxyribose sugars form part of the structure framework of RNA and DNA.

(3) polysaccharides are structural elements in the cell walls of bacteria and plants. Cellulose, the main constituent of plant cell walls, is one of the most abundant organic compounds in the biosphere.

CarbohydratesDefinition: carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups.

Function: (1) serves as energy stores, fuels,and metabolic intermediates.

(2) ribose and deoxyribose sugars form part of the structure framework of RNA and DNA.

(3) polysaccharides are structural elements in the cell walls of bacteria and plants. Cellulose, the main constituent of plant cell walls, is one of the most abundant organic compounds in the biosphere.

(4) carbohydrates are linked to many proteins and lipids, where they play key roles in mediating interactions among cells and interactions between cells and other elements in the cellular environment.

Monosaccharides are aldehydes or ketones with multiple hydroxyl groups

The simplest carbohydrates

D-Ketoses containing three, four, five, and six carbon atoms

Asymmetric center

D-Aldoses containing three, four, five, and six carbon atoms

Asymmetric center

The predominant forms of ribose, glucose, fructose, and many other sugars in solution are not open chains. Rather, the open-chain forms of these sugars cyclize into rings.

The predominant forms of ribose, glucose, fructose, and many other sugars in solution are not open chains. Rather, the open-chain forms of these sugars cyclize into rings.

Where does the ring come from?

An aldehyde can interact with alcohol to form hemiacetal

A ketone can interact with alcohol to form hemiketal

Pentose and hexoses cyclize to form furanose and pyranose ring

The C-5 hydroxyl group attacks the oxygen atom of the C-1 aldehyde group to form an intromolecular hemiacetal.

Pentose and hexoses cyclize to form furanose and pyranose ring

The C-5 hydroxyl group attacks the oxygen atom of the C-2 ketone to form an intromolecular hemiketal.

Fructose can form both five-membered frunose

and six-membered pyranose rings

RNA DNA

deoxyribonucleic acidribonucleic acid

Conformation of pyranose ring

The chair form of b-D-glucopyranose predominates because all the axial positions are occupied by hydrogen atoms. The bulkier –OH and -CH2OH groups emerge at the less-hindered periphery.

The boat form of glucose is disfavored because of the steric hindrance

Monosaccharides can be modified by reaction

with alcohols and amines to form adducts

O-Glycosidic bond: between the anomeric carbon atom of glucose and the hydroxyl oxygen atom of methonol.

N-Glycosidic bond: anomeric carbon atom – nitrogen atom of an amine

Carbonhydrates can be modified by the addition of substituents. Such modified carbohydrates are often expressed on cell surface

Complex carbonhydrate are formed by linkage of monosacchrides

Oligosaccharides

O-glycosidic bonds

Monosaccharides

Sucrose, lactose, and maltose are the common disaccharides

from dietary components

2 monosaccharides

Disaccharides

Glycosidic bond

enzyme

sucrase

lactase

maltase

Sucrose, lactose, and maltose are the common disaccharides

from dietary components

Electron micrograph of a microvillus

lactose

Monosaccharides

Oligosaccharides

Glycosidic bond

Glycosyltransferase

Glycosyltransferase specifically catalyze the formation of glycosidic bonds, that means each enzyme must be specific to the sugars being linked.

Glycosyltransferase

Carbonhydrates can be attached to ptroteins to form glycoproteins

Carbonhydrates can attach to ptroteins forming glycoproteins

Glycosidic bonds between proteins and carbohydrates

Note

1. Carbohydrates may be linked to proteins through asparagine (N-linked) or through serine or threonine (O-linked) residues.

2. An asparagine residue can accept an oligosacchride only if the residue is part of an Asn-X-Ser or Asn-X-Thr sequence.

3. Potential glycosylation sites can be detected within amino acid sequences.

Elastase, showing linked carbohydrates on its surface

Protein Glycosylation takes place in the lumen of the ER and the Golgi complex

Transport into the endoplasmic reticulum

1. A signal sequence directs the nascent protein through channels in the ER membrane and into the lumen.

2. The N-linked glycosylation begins in the ER and continues in the Golgi complex, whereas the O-linked glycosylation takes place exclusively in the Golgi.

Bonifacino JS and Glick BS, 2004

1. Terminal glycosylation: carbohydrate processing in the

Golgi apparatus.

2. Core glycosylation: takes place in the ER.

3.Tremendous structural diversification can occur as a

result of the terminal glycosylation process.

Formation of a mannose 6-phosphate

1. Mannose 6-phosphate is a marker directing certain proteins from the Golgi to lysosomes.

2. Deficient in the phosphotransferase

cell disease

(psychomotor retardation + skeletal deformities)

Can’t form mannose 6-phosphate

Mistargeting of essential enzymes

(lysosome blood and urine)

Lectins, a specific carbohydrate-binding proteins mediating cell-cell interactions

Structure of a C-type carbohydrate-binding domain from an animal lectin

Selectins (a member of C-type lectin) mediate cell-cell interactions

lymphocyte

Lining of lymph-node

Summary

1. Monosaccharides are aldehydes or ketones with multiple hydroxyl groups.

2. Complex carbohydrates are formed by linkage of monosacchrides.

3. Carbohydrate can attach to proteins to form glycoproteins.

4. Lectins are specific carbohydrate-binding proteins.

Selected readings:

Sharon N and Lis H. 1993. Carbohydrates in cell recognition. Sci. Am. 268: 82-89.

Woods RJ. 1995. Three-dimensional structures of oligosaccharides. Curr. Opin. Struct. Biol. 5: 591-598.

Fukuda M and Hindsgaul O. 2000. Molecular Glycobiology. IRL Press at oxdord University Press.

Berg JM et al. Biochemistry. 2002. W. H. Freeman and Company.