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Chapter 1 Amino Acids to Proteins

1.1 Protein Composition

1.2 Protein Conformations

1.3 Protein Structure and

Function: A Few Examples

1.4 The Dynamics of Proteins

1.5 Experiments

1.1 蛋白质的组成

1.2 蛋白质的构象

1.3 蛋白质的结构与 功能：几个例子

1.4 蛋白质动力学

1.5 实验研究

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Chapter 1 Amino Acids to Proteins第 1 章 氨基酸到蛋白质

Life is most directly the

work of proteins.

Proteins allow organisms

to grow and reproduce.

They provide shape,

strength and movement.

In the cell, proteins are

everywhere and do

almost everything.

生命几乎就是蛋白质的杰作。蛋白质让生物可以生长和繁殖。它们为生物提供了外形和力量，以及运动功能。在细胞中，蛋白质无处不在，行使着几乎任何功能。

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1.1 Protein Composition / 蛋白质的组成

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Glycine 甘氨酸 Gly G

Alanine 丙氨酸 Ala A

Isoleucine 异亮氨酸 Ile I

Leucine 亮氨酸 Leu L

Methionine 甲硫氨酸 Met M

Phenylalanine 苯丙氨酸 Phe F

Tryptophan 色氨酸 Trp W

Proline 脯氨酸 Pro P

Valine 缬氨酸 Val V

Serine 丝氨酸 Ser S

Threonine 苏氨酸 Thr T

Asparagine 天冬酰胺 Asn N

Glutamine 谷氨酰胺 Gln Q

Cysteine 半胱氨酸 Cys C

Tyrosine 酪氨酸 Tyr Y

Aspartic acid 天冬氨酸 Asp D

Glutamic acid 谷氨酸 Glu E

Arginine 精氨酸 Arg R

Histidine 组氨酸 His H

Lysine 赖氨酸 Lys K

Hydrophobic R groups 疏水的R基团 Hydrophilic R groups 亲水的R基团

Acidic R groups 酸性的R基团Basic R groups 碱性的R基团

9 6

23

The twenty amino acids and their abbreviation

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Structures of hydrophobic amino acids

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Structures of the hydrophilic amino acids

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Structures of the 20 common amino acids

Negative charge Positive charge

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The formation of a peptide bond

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Partial double bond / 部分双键

C

O

N

H

C

O-

N+

H

Partial double bond

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Rigid and flexible bonds

3D structure

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N-terminus and C-terminus / N- 末端和 C- 末端

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1.2 Protein Conformations / 1.2 蛋白质的构象

1.2.1 Describing Protein

Structure

1.2.2 Chemical and

Physical Basis

for Protein Folding

1.2.1 描述蛋白质 的结构

1.2.2 蛋白质折叠的 化学和物理基础

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1.2.1 Describing Protein Structure

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α helix / α 螺旋H

N

HC

C

R2

O

H

N

HC

R5

C

O

(a) (b)

Hydrogen bond

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β sheet / β 折叠

Hydrogen bond

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Parallel and antiparallel β sheets

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Tertiary structure / 三级结构

αhelix

βsheet

Turn

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Quaternary structure / 四级结构

One subunit

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Physical interactions involved in

protein folding

1) Covalent bonding

2) Hydrogen bonding

3) Ionic bonding

4) Van der Waals forces

5) Hydrophobic interaction

1.2.2 Chemical and Physical Basis for Protein Folding

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1) Covalent bond / 共价键

Sharedelectrons

H－ H

H +1 H+1

+1 +1

Covalent bond

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Covalent bond / 共价键

A

GI

LM

F W

N

P V

S

T

Q

C

YD

E R

H

K

G

I

K

A

F

W

EI

Covalent bond

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Covalent bond / 共价键

Covalent bond

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2) Hydrogen bond / 氢键

δ +H

O

H δ +

δ

δ +H

O

H δ +

δ

δ + H

O

H δ +

δHydrogen bond

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Partial charges vs. Full charges

Na+11

Cl+17

Cl

δ–

δ+δ+

Na

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Hydrogen bond / 氢键

Hydrogen bond

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3) Ionic bond / 离子键

The ionic bond of sodium chloride, NaCl

Na+11

Cl+17

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Ionic bond / 离子键

Glu

C

COO━

HH3N+

C

COO━

HH3N+

CH2

C

O

CH2

O━

Lys

C

COO━

HH3N+

C

COO━

HH3N+

CH2

CH2

CH2

CH2

NH3+

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4) Van der Waals forces / 范德华力

Atom 1 Atom 2

van der Waals force

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Van der Waals forces vs. Ionic bond

Atom 1 Atom 2

Van der Waals forces• The atom itself has negativ

e and positive parts• The interaction is transient

Ionic bond• The whole atom is either

negative or positive• The interaction is stable

Atom 1 Atom 2

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Van der Waals forces vs. hydrogen bond

Atom 1 Atom 2

Van der Waals forces• The atom itself has negativ

e and positive parts• The interaction is transient

Hydrogen bond• The whole atom is either

partially negative or positive

• The interaction is stable

Atom 1 Atom 2

δ–δ+

δ–δ+

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5) Hydrophobic interaction

?

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Nonpolar molecules are forced together

Water molecules get contacts with each other.

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Hydrophobic interaction / 疏水相互作用

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1.3 Protein Structure and Function

carbonic anhydrase

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Actin / 肌动蛋白

(a)

(b) An actin monomer

An actin filament

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Kinesin / 驱动蛋白

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1.4 The Dynamics of Proteins

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Induced-fit vs. lock-and-key models

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ATP synthetase / ATP 合成酶

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Allosteric regulation / 别构调节

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lac repressor / lac阻遏蛋白

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1.5 Experiments / 1.5 实验研究

dialyse

dialysis