chap 1.1 to 1.2

1

chap 1.1 to 1.2 1

自然科學自然科學自然科學自然科學 數學數學數學數學

1.1.1.1.物理科學物理科學物理科學物理科學

requirerequirerequirerequire

((((研究物質及能量研究物質及能量研究物質及能量研究物質及能量))))

地質學

地質學

地質學

地質學

物理學

物理學

物理學

物理學

天文學

天文學

天文學

天文學

化學化學化學化學

跨領域跨領域跨領域跨領域

跨領域跨領域跨領域跨領域

分析化學

分析化學

分析化學

分析化學

物理化學

物理化學

物理化學

物理化學

有機化學

有機化學

有機化學

有機化學

無機化學

無機化學

無機化學

無機化學

物理化學物理化學物理化學物理化學

化學物理化學物理化學物理化學物理

原子分子原子分子原子分子原子分子 生物物理化學生物物理化學生物物理化學生物物理化學

醫學化學醫學化學醫學化學醫學化學

生物化學生物化學生物化學生物化學

2.2.2.2.生物生物生物生物科學科學科學科學

動動動動物學物學物學物學

植植植植物學物學物學物學

微生物學

微生物學

微生物學

微生物學

生態學

生態學

生態學

生態學

遺傳學

遺傳學

遺傳學

遺傳學

生理學

生理學

生理學

生理學

科學的範疇科學的範疇科學的範疇科學的範疇

chap 1.1 to 1.2 2

化學與物理化學與物理化學與物理化學與物理

量子力學量子力學量子力學量子力學(quantum mechanics)

本世紀初本世紀初本世紀初本世紀初，，，，量子力學肇始並宣稱已解決量子力學肇始並宣稱已解決量子力學肇始並宣稱已解決量子力學肇始並宣稱已解決所有的化學問題及一半的物理問題所有的化學問題及一半的物理問題所有的化學問題及一半的物理問題所有的化學問題及一半的物理問題

Schrodinger Equation：：：：ΗΨΗΨΗΨΗΨ=ΕΨΕΨΕΨΕΨΗΗΗΗ：：：：Hamiltonian operator

ΨΨΨΨ：：：：wavefunction

ΕΕΕΕ：：：：energy

所有的分子性質所有的分子性質所有的分子性質所有的分子性質、、、、化學反應皆可由此化學反應皆可由此化學反應皆可由此化學反應皆可由此Schrodinger Equation推測推測推測推測

然而現今只能成功地推測小分子然而現今只能成功地推測小分子然而現今只能成功地推測小分子然而現今只能成功地推測小分子！！！！！！！！

chap 1.1 to 1.2 3

化學與應用化學化學與應用化學化學與應用化學化學與應用化學

•材料科學材料科學材料科學材料科學：：：：金屬材料金屬材料金屬材料金屬材料

高分子材料高分子材料高分子材料高分子材料

電子工程電子工程電子工程電子工程：：：：電子材料電子材料電子材料電子材料

化學工程化學工程化學工程化學工程：：：：將化學實驗室的製程放大將化學實驗室的製程放大將化學實驗室的製程放大將化學實驗室的製程放大

食品食品食品食品：：：：食品添加物食品添加物食品添加物食品添加物

生化及藥化產業生化及藥化產業生化及藥化產業生化及藥化產業：：：：製藥製藥製藥製藥、、、、生物科技生物科技生物科技生物科技

chap 1.1 to 1.2 4

Chapter 1Foundations of Biochemistry

What is Chemistry？？？？This science that tries to understand：：：：(A)The properties of substances

(B)The changes that substances undergo

The realm of substances：：：：(A)Natural substances：：：：e.g.water, air, element, salt...

(B)New compounds created by chemists

e.g.polymer ,nylon...

(C)Chemicals found in living creatures：：：：e.g.DNAs, proterins, carbohydrates...

Biochemistry tries to understand：：：：(A)The properties of biomolecules

(B)The changes that biomolecules undergo

chap 1.1 to 1.2 5

1. A high degree of chemicail complexity &

microscopic organization

2. Living organisms extract, transform,and use

“energy” from their environments, usually in the

form of chemical nutrients or sunlight.

3. Defined functions for each of an organism’s

components and regulated interactions among

them

4. Mechanisms for sensing and responding to

alterations in their surrounding

5. Living organisms are capable of “self-assemby”

and self-replication

6. A capacity to change over time by gradual

evolution

The differences between livings and inanimate objects

chap 1.1 to 1.2 6

Biochemistry explains diverse forms of life in

unifying chemical terms：：：：

Living organisms are remarkably alike at the

cellular and chemical levels

Living organisms are enormously diverse：：：：

animals、、、、plants

同同同同((((微觀微觀微觀微觀))))異異異異((((巨觀巨觀巨觀巨觀))))

Biochemistry describes：：：：1.The structures, mechanisms, and chemical processes

shared by all organisms in “molecular terms”

2.Provides organization principles that underlie life

The molecular logic of life

chap 1.1 to 1.2

2

chap 1.1 to 1.2 7

The molecular logic of life

• Consider the properties of living organisms

• Describe a set of principles that characterize

all living organism

Diverse living organisms

share common chemical

features chap 1.1 to 1.2 8

Cells:

1. Plasma membrane：：：：

defines the periphery of the

cell, separating its contents

from the surroundings.

It is composed of lipid and

protein molecules that form

a thin, tough, pliable,

hydrophobic barrier

around the cell.

1.1 Cellular Foundations

Cells are the structural and functional units of all living organisms

chap 1.1 to 1.2 9

2. Cytoplasm：：：：

composed of cytosol and

suspended particles

Cytosols：：：：

enzymes, RNA molecules,

monomeric subunits (amino

acids and nucleotides),

metabolites (small organic

molecules), coenzymes.

suspended particles：：：：

Supramolecular structures

(like ribosomes and

proteasomes)chap 1.1 to 1.2 10

3. Nucleus or Nucleoid：：：：

Complete set of genes (genome)

Eukaryotes (真核生物真核生物真核生物真核生物)：：：：

Cells with nuclear envelopes

Prokaryotes (原核生物原核生物原核生物原核生物)：：：：without nuclear envelopes

chap 1.1 to 1.2 11

• Animal and plant cells are 5 to 100 µµµµm in diameter

• many bacteria are only 1 to 2 µµµµm long

• the smallest cells：：：：mycoplasmas (黴漿菌黴漿菌黴漿菌黴漿菌), ~300nm in

diameter, and ~10-14 ml in volume

•Upper limit of cell size：：：：defined by the rate of diffusion

of solute molecules in aquaous systems

•Lower limit of cell size：：：：Set by the minimum number of

each type of biomolecule (supramolecules and organelles)

required by the cell (e.g. ribosome，，，，~20nm long)

Cellular Dimensions Are Limited by Oxygen

Diffusion

chap 1.1 to 1.2 12

There Are Three Distinct Domains of Life

1. bacteria (真細菌真細菌真細菌真細菌)inhabits soils, surface waters, tissues.

e.g. E. Coli

2. Archaea (古細菌古細菌古細菌古細菌)inhabits more extreme environments (salt lakes, hot

springs…) e.g. methanococcus jannasch

3.Eukaryotes (真核生物真核生物真核生物真核生物)

chap 1.1 to 1.2

3

chap 1.1 to 1.2 13

prokaryotes包含兩個包含兩個包含兩個包含兩個Groups

1. bacteria(真細菌真細菌真細菌真細菌)

2. archaea (古細菌古細菌古細菌古細菌)

There Are Three Distinct Domains of Life

chap 1.1 to 1.2 14

Organisms can be classified according to their

energy source (sunlight or oxidizable chemicals)

chap 1.1 to 1.2 15

Escherichia coli (大腸大腸大腸大腸桿菌桿菌桿菌桿菌) is the most-studied

prokaryotic cell : 5 µµµµm in length; 2 µµµµm in diameter

ribosomes

membrane 伸伸伸伸

出出出出：：：：

Pili, flagella

chap 1.1 to 1.2 16

Escherichia coli is the most-studied

prokaryotic cell

•cytoplasm：：：：Ribosomes (15,000個個個個), enzymes (1000種種種種),

metabolites, and cofactors

•Nucleoid：：：：A single, circular molecule of DNA. 1000x

length(v.s. cell)，，，，packed 成成成成1 µµµµm左右大小左右大小左右大小左右大小•Plasmid：：：：Few smaller, circular molecule of DNA

Resistance to toxins and antibiotics.Amenable

to manipulation for molecular genetic study

chap 1.1 to 1.2 17

Cell envelopes：：：：

• Gram-negative bacteria (e.g. E. Coli, cyanobacteria氰氰氰氰

菌菌菌菌, etc)

with outer membrane

peptidoglycan layer

extensive inner membrane system

• Gram-postive bacteria (e.g. Bacillus subbtilis桿菌桿菌桿菌桿菌,

staphylococcus aureus葡萄球菌葡萄球菌葡萄球菌葡萄球菌, archaebacteria, etc.)

without outer membrane

pseudopeptidoglycan layer thicker

inner membrane

Escherichia coli is the most-studied

prokaryotic cell

chap 1.1 to 1.2 18

Cell envelopesGram negative and positive bacteria

chap 1.1 to 1.2

4

chap 1.1 to 1.2 19

Typical Eukaryotic cells

5-100 μμμμm

Eukaryotic Cells Have a Variety of Membranous

Organelles, Which Can Be Isolated for Study

核仁核仁核仁核仁

chap 1.1 to 1.2 20

Plant cell

Eukaryotic Cells Have a Variety of Membranous

Organelles, Which Can Be Isolated for Study

堆疊堆疊堆疊堆疊

葉綠體葉綠體葉綠體葉綠體

澱粉細粒澱粉細粒澱粉細粒澱粉細粒

類囊體類囊體類囊體類囊體

chap 1.1 to 1.2 21

Eukaryotic Cells Have a Variety of Membranous

Organelles, Which Can Be Isolated for Study

chap 1.1 to 1.2 22

Plasma membrane：：：：Lipid bilayer, contains transporter and receptors

1.Transporters：：：：proteins that span the membrane and

carry nutrients into the cell and products out

2.Signal receptors：：：：bind with extra-cellular signaling

molecules (ligands): receptors recognize ligands (can be small

molecules or macromolecules).

e.g. drugs – receptor

virus/bacteria/protein – receptors

antigens - antibody

•Higher plants have cell wall(rigid, protective shell)

formed by cellulose & carbohydrate polymers outside

the plasma membrane

Eukaryotic Cells Have a Variety of Membranous

Organelles

補充

chap 1.1 to 1.2 23

Endoplasmic reticulum(ER)：：：：

Highly convoluted, three-dimensional network of

membrane-enclosed spaces throughout the cytoplasm

and enclosing a subcellular compartment(the lumen of

the ER)

Rough ER：：：：

Granular appearance (because ribosomes attached)

Smooth ER：：：：

1. the site for lipid synthesis

2. metabolism of certain drugs and toxic compound

3. In some tissues(e.g skeletal muscle), storage and

release Ca+2

Cellular Components of Eukaryotic Cells補充

chap 1.1 to 1.2 24endocytosis exocytosis

Rough ER

Golgi complex

smooth ER

補充

chap 1.1 to 1.2

5

chap 1.1 to 1.2 25

Golgi complex：：：：

• Cis side：：：：face rough ER

• Medial element

• Trans side：：：：face plasma membrane

• Proteins will be modified (e.g. adding sulfate, lipid,

carbohydrate groups)

補充

chap 1.1 to 1.2 26Proteins(during the synthesison ribosomes on rough ER)

Inserted into rough ER lumen

Move to the Golgi complex(Proteins will be modified e.g. adding sulfate, lipid, carbohydrate groups)

Bud

1.Targeted for intracellular organelles(e.g. lysosomes)2.Released from the cell byexocytosis3.Incorporate into plasma membrane

Small membrane vesicles(Transport vesicles)

補充

chap 1.1 to 1.2 27

Ribosome：：：：

• Synthesis of proteins

• Ribosomes attached ER synthesis protein that will

be：：：：

1.Released from the cell(secretory proteins)

2.Targeted for intracellular organelle(e.g. lysosome)

3.Inserted into nuclear or plasma membranes

• Cytoplasmic ribosomes synthesize proteins that will

remain and function in cytosol

補充

chap 1.1 to 1.2 28

Lysosomes(溶溶溶溶酶酶酶酶體體體體)：：：：(Only in animal cells)

• contain enzymes, capable of digesting proteins,

polysaccharides, nucleic acids, and lipids.

• act as recycling centers

分解分解分解分解：：：：complex molecules carried from endocytosis

foreign cell fragment carried from phagocytosis

organelles carried from cell’s cytoplasm

分解成分解成分解成分解成 a.a, monosaccharides, fatty acids.

• pH of lysosomal compartment < 5

enzymes inside are more active in acidic pH

補充

chap 1.1 to 1.2 29

Peroxisomes(過氧化氫過氧化氫過氧化氫過氧化氫酶酶酶酶體體體體)：：：： contain catalase

2H2O2 2H2O +O2

catalase

Glyoxysomes(乙醛酸循環體乙醛酸循環體乙醛酸循環體乙醛酸循環體)：：：：

• specialized peroxisomes in certain plant cells

• contain high conc. of enzymes of glyoxylate cycle

fats Carbohydrates

enzymes

Lysosomes, peroxisomes, and glyoxysomes

稱稱稱稱為為為為 microbodies

補充

chap 1.1 to 1.2 30

Vacuoles of plant cells

• plant cells have no lysosomes.

• vacuoles carry similar “degradative” rx

•Tonoplast (the membrane surrounding the vacuole):

regulate the entry of ions, metabolites etc. for

degradation.

•Vacuole (at acidic pH) : degrade and recycle

biomolecules 的的的的enzymes

•Vacuoles also provide physical support to the plant

cell.(因因因因salt含量比含量比含量比含量比cytosol高高高高，，，，產生產生產生產生osmotic pressure or

call turgor pressure 將將將將cell撐起撐起撐起撐起)

•Vacuoles 含染料含染料含染料含染料，，，，會使花果有顏色會使花果有顏色會使花果有顏色會使花果有顏色

補充

chap 1.1 to 1.2

6

chap 1.1 to 1.2 31

Nuclear Pore

Nucleolus

補充

chap 1.1 to 1.2 32

Nucleus：：：：contains the genome

•Nuclear pores(～～～～90 nm in diameter) associated with

nuclear pore complexes specific transporters

Chromatin(染色質染色質染色質染色質)：：：：contain DNA and proteins (histones)

bound tightly together

Nucleolus：：：：在在在在nucleus中中中中，，，，含含含含many copies of the genes

coding ribosomal RNAs (有效地有效地有效地有效地transcribe into ribosomal

RNA！！！！)以備有效產生許多以備有效產生許多以備有效產生許多以備有效產生許多ribosomes！！！！

enzymes for

DNA replication

DNA repair

transcription

RNA processing

to nucleoplasm to cytoplasm

mRNA precursors

and associated proteins

補充

chap 1.1 to 1.2 33

Mitosis：：：：Nuclear division 有絲分裂有絲分裂有絲分裂有絲分裂

Cytokinesis：：：：細胞分裂細胞分裂細胞分裂細胞分裂, 胞質分裂胞質分裂胞質分裂胞質分裂(cell division)

Double helix

Nucleosomes (DNA + histones) 1：：：：1 ratio(重量比重量比重量比重量比)

Chromatin fiber

Chromatid

正在正在正在正在mitosis時時時時，，，，mitotic chromosome

(含含含含two identical chromatid)

106個個個個帶帶帶帶－－－－電電電電 帶帶帶帶＋＋＋＋電的電的電的電的protein

補充

chap 1.1 to 1.2 34

Somatic cells(體細胞體細胞體細胞體細胞)：：：：

have two copies of each chromosome (diploid,雙倍的雙倍的雙倍的雙倍的)

Gametes(配子配子配子配子) (egg, sperm 生殖細胞生殖細胞生殖細胞生殖細胞):

•have only one copy of each chromosome (haploid, 單倍的單倍的單倍的單倍的)

•有性生殖時與不同性的配子合成有性生殖時與不同性的配子合成有性生殖時與不同性的配子合成有性生殖時與不同性的配子合成 zygate (合子合子合子合子)

DNA of a single diploid human cell

拉長時拉長時拉長時拉長時：～：～：～：～2m

packed時時時時：～：～：～：～200μμμμm

104差別差別差別差別

補充

chap 1.1 to 1.2 35

•1μμμμm in size

•數百數百數百數百～～～～1000個個個個 mitochondria / eukaryotic cell

•含含含含two membrane：：：：

outer membrane

inner membrane (called cristae)：：：：

內含物內含物內含物內含物(matrix)：：：：enzymes involving in the energy-

yielding metabolism.

利用利用利用利用oxidation of organic nutrients

製造製造製造製造ATP

Mitochondria are the power plants of

Aerobic Eukaryotic cells

產生能量產生能量產生能量產生能量

補充

chap 1.1 to 1.2 36

• mitochondria are produced only by division of

previously existing mitochondria.

• mitochondria contains its own DNA, RNA, and

ribosomes.

• mitochondria DNA codes for certain proteins specific

the mitochondria inner membrane.

Mitochondria are the power plants of

Aerobic Eukaryotic cells

補充

chap 1.1 to 1.2

7

chap 1.1 to 1.2 37

Pigment molecules (chlorophyll,葉綠素葉綠素葉綠素葉綠素)

adsorb solar light

make ATP

reduce CO2 to carbohydrates：：：：

在在在在chloroplast的的的的inner membranes (thylakoid類粒體類粒體類粒體類粒體)

Mitochondria and chloroplast probably evolved from

endosymbiotic bateria (內共生菌內共生菌內共生菌內共生菌).

Chloroplast(葉綠體葉綠體葉綠體葉綠體)：：：：power plants of plant cells

補充

chap 1.1 to 1.2 38

Cytoskeleton：：：：

1. actin filaments 6nm

(又叫又叫又叫又叫microfilament 肌動蛋白絲肌動蛋白絲肌動蛋白絲肌動蛋白絲)

2. microtubules 22nm

(微管微管微管微管)

3. intermediate filaments 6-22nm

Cytoskeletal components

Simple protein subunits that polymerize

(location in cells, not rigidly fixed, change during

mitosis, cytokinesis….)

The Cytoplasm is organized by the

cytoskeleton and is highly dynamic

constantly disassemble & reassemble

chap 1.1 to 1.2 39

Microtubules radiating

from the cell centers

Intermediate filaments

Extended throught the

cytoplasm

Actin filaments

bundled together to

form ‘stress fibers’chap 1.1 to 1.2 40

The Cytoplasm is organized by the cytoskeleton and

is highly dynamic

cytoskeletal filaments:

1. Actin filaments (in red)

2. Microtubules (in green)

nucleus (in blue)

(A)

chap 1.1 to 1.2 41

The Cytoplasm is organized by the cytoskeleton and

is highly dynamic(B)

cytoskeletal filaments:

2. Microtubules (in green)

3. Intermediate filaments

( in red)

Chromosome (in blue)

chap 1.1 to 1.2 42

Actin sununits

actin thin filament

parallelly-linked(by fordin)

cross-linked(by filamin)

＋＋＋＋filamin ＋＋＋＋fordin

actin filament

Actin filament

head(binds to actin filament)

tail(binds to the membrane of a

cytoplasmic organelle)

+Myosin

+ ATP

move cytoplasmic organelle or vesicle along the actin

filament (called cytoplasmic streaming)

(1) Actin(肌動蛋白肌動蛋白肌動蛋白肌動蛋白) filament (or microfilament): 6-7nm

chap 1.1 to 1.2

8

chap 1.1 to 1.2 43

*muscle contraction 亦相似亦相似亦相似亦相似

Actin filament+

Myosin+

ATP

muscle contraction

(See figure 5-31)

(2)microtubles (22nm)

subunits：：：：αααα- & ββββ- tubulin

(throughout the cell, but concentrated around nucleus)

mitosis時時時時, microtubules 會會會會 highly organized & help

the separation of chromosomes (可能可能可能可能provide motive

force)chap 1.1 to 1.2 44

Microtubules+

kinesin

dynesin+

ATP

move organelle along microtubules (以以以以1μμμμm/s移動移動移動移動)

e.g. cilia

flagella beating motion

e.g.

•contraction of muscle

propelling action of cilia

and flagella

• intracellular transport

of organelles

reason：：：：myosin, kinesin,dynesin

splitting “ATP”

driving sliding motion along

microtubules and

microfilaments

chap 1.1 to 1.2 45

(3)Intermediate filaments (8-10nm)：：：：provide internal mechanical support for the cell and

to position its organelles

subunit：：：： vimentin, keratin,desmin等等等等

e.g. 在在在在endothelial cells(內皮細胞內皮細胞內皮細胞內皮細胞), vimentin

fibers anchor nucleus and fat droplets in

the specific location

• The cytoplasm is crowded, highly organize and dynamic!!

• Cytoplasm：：：：meshwork of structural fibers (protein fibers)

membrane-bound organelles locate在其中在其中在其中在其中

chap 1.1 to 1.2 46

Endocytosis and Exocytosis carry traffic across

the plasma membrane

Endocytosis(胞飲胞飲胞飲胞飲)：：：：

A mechanism for transporting components of the

surrounding medium deep into the cytoplasm

Phagocytosis(吞噬吞噬吞噬吞噬)：：：：

One kind of endocytosis，，，，but carry cell fragment or

other smaller cells

Exocytosis (胞吐胞吐胞吐胞吐)：：：：

A vesicle in the cytoplasm moves to the inside surface

of the plasm membrane fuses with it, then release the

contents outside the membrane

chap 1.1 to 1.2 47

Cells Build Supramolecular Structures

(A)Protein：：：：

20種種種種amino acids as building blocks

chap 1.1 to 1.2 48

Cells Build Supramolecular Structures

(B)DNA：：：：4 possibilities

5’ 3’

chap 1.1 to 1.2

9

chap 1.1 to 1.2 49

+ Fatty acids

(C)Lipids

e.g. Oleate

palmitate

Glycerol

R1

R2

R3

可形成可形成可形成可形成Lipid bilayer

chap 1.1 to 1.2 50

(D)Polysaccharides

Most abundant polysaccharides：：：：starches, glycogen and

cellulose

Monomeric subunit：：：：主要為主要為主要為主要為glucose

chap 1.1 to 1.2 51

Structural hierarchy in the molecular organization of

cells

chap 1.1 to 1.2 52Building blocks

Covalent bonds

Macromolecules

Supramolecular assemblies

Organelles

Cell

Amino acids

Nucleotides

Sugars

ProteinsDNARNAPolysaccharides

MembranesRibosomes

Chromatin

Microtubules

Nucleus

Mitochondria

Golgi body

E.R

etc

Non-covalent interactions

Hydrogen bondIonic interaction

Hydrophobic interaction

Structural hierarchy in the molecular organization of cells

Van der Waals forces

chap 1.1 to 1.2 53

Complexity of life Simplicity of “element”world

1.2 Chemical Foundations

Bulk elements：：：：required in gram(only H, C, N, O, Na,

P, S, Cl, K, Ca, in red) 佔佔佔佔99%99%99%99%

Trace elements：：：：required much less (colored in yellow)

如如如如Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Mo, Ichap 1.1 to 1.2 54

組成組成組成組成biomolecule的骨架的骨架的骨架的骨架Covalent bonding

O

H

H H

N

H H

C

H

H

H

H

S

H

H P

O

O

H

O

H

O

H

Geometry of

Carbon Bonding

C CBond length

1.54A

chap 1.1 to 1.2

10

chap 1.1 to 1.2 55

Biomolecules Are Compounds of Carbon

with a Variety of Functional Groups

Some common functional

groups of biomolecules

Multi-functionalMany biomolecules

“reactivity (chemical properties) of

biomolecules determined by: (1) functional

groups, (2) 3-dimensional structure

e.g. glycine(R=H)

amino

carboxylchap 1.1 to 1.2 56

chap 1.1 to 1.2 57

• In cytosol:a collection of a thousand of small

molecules (Mr ~ 100 to 500), the central

metabolites in the major pathway in cells.

• including amino acids, nucleotides, sugars, etc.

Polar or charged, in µµµµM to mM

• may contain secondary metabolites (in specific

plant cells that gives plants characteristic scents,

e.g morphine, caffeine etc)

Cells contain a universal set of small

molecules

chap 1.1 to 1.2 58

Macromolecules Are the Major Constituents of Cells

Proteins and nucleic acids are informational

macromolecules

chap 1.1 to 1.2 59

Three-Dimensional Structure Is Described

by Configuration and Conformation

Three ways to represent the structure of Biomolecules：：：：

(a) Structure Formula

(b) Ball-and-stick model (shows relative bond length and

bond angles

(c) Space-filling model (shows correct 電子密度的電子密度的電子密度的電子密度的bond length)chap 1.1 to 1.2 60

Configuration －－－－changed only by bond-breaking

Configuration ：：：：fixed spatial arrangement of atoms in a

molecule

In the presence of (1) double bonds (2) chiral center

configurational isomers

chap 1.1 to 1.2

11

chap 1.1 to 1.2 61

respected to

double bond

geometric

isomers

or cis-trans

chiral centers

enantiomers

diastereomers

stereoisomersR/S form

D/L form

(mirror images)

(non-mirror images)

n 個個個個 Chiral carbons 2n個個個個 stereoisomers

Configurational isomers can be isolated (if use proper

separating methods)有有有有chiral center，，，，表四個不同的表四個不同的表四個不同的表四個不同的atom，，，，C的四周圍電子密度不的四周圍電子密度不的四周圍電子密度不的四周圍電子密度不均勻均勻均勻均勻，，，，使電磁波偏移使電磁波偏移使電磁波偏移使電磁波偏移• Enantiomers will notate the plane of plane-polarized light

• Racemic mixtures(equimolar mixture of two enantiomers)

will not rotate the plane-polarized light chap 1.1 to 1.2 62

Molecular Conformation is Changed by Rotation

about Single Bonds

Molecular conformation

The spatial arrangement

of substituent groups can

be changed by “free

rotation”(w/o any bond

breaking)

See figure 1-21

Potential energy differences of

many conformations of ethane

Energy differences are two

small conformational isomers

can be interconverted

Cannot be separated

chap 1.1 to 1.2 63

Configuration and conformation define biomolecular

Structures

Molecular recognition：：：：related to their three-dimensional

structures (結構上的互補性結構上的互補性結構上的互補性結構上的互補性, complementarity)

e.g. Hormone molecule with receptor

Antigen with a specific antibody

Substrate with the catalytic site of an enzyme

TAR region of HIV

genome w/arginine

Example: Fig. 1-22

chap 1.1 to 1.2 64

Interactions between Biomolecules are stereospecific

In vivo, biomolecules are usually present in only one

of their chiral forms.

Glucose Only D form

Amino acids Only L isomerse.g.

Enzymes have the ability to distinguish between

isomers. (Enzymes are stereospecific！！！！)

Example: Fig. 1-23

chap 1.1 to 1.2 65

(a)Carvone：：：：Smell as spearmint (R form)

caraway香菜香菜香菜香菜 (S form)

Smell sensory receptor can

distinguish！！！！

(b) aspartame：：：：Taste sweet

taste receptor can distinguish！！！！

aspartame