生物化学英文课件Biochemistry-chapter 3
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生物化学(英文版)biochemistry-chapter1英
Secondary structure
Through biochemical research, people can understand the basic processes and mechanisms of organisms, explore the mechanisms of disease occurrence and development, and provide scientific basis for disease prevention, diagnosis, and treatment.
Biochemistry is an interdisciplinary field that aims to reveal the chemical essence behind life phenomena.
Definition of Biochemistry
Biochemistry helps to increase crop yield and improve quality in agriculture, and contributes to the development of nutritious, safe, and reliable new types of food in the food industry.
Large molecules in living organisms, such as proteins, nucleic acids, and polysaccharides, all have carbon as their core.
Carbon atoms can form complex network structures through covalent bonds, which endow biomolecules with high diversity and stability.
Through biochemical research, people can understand the basic processes and mechanisms of organisms, explore the mechanisms of disease occurrence and development, and provide scientific basis for disease prevention, diagnosis, and treatment.
Biochemistry is an interdisciplinary field that aims to reveal the chemical essence behind life phenomena.
Definition of Biochemistry
Biochemistry helps to increase crop yield and improve quality in agriculture, and contributes to the development of nutritious, safe, and reliable new types of food in the food industry.
Large molecules in living organisms, such as proteins, nucleic acids, and polysaccharides, all have carbon as their core.
Carbon atoms can form complex network structures through covalent bonds, which endow biomolecules with high diversity and stability.
生物化学英文课件Biochemistry-chapter 3
Requirement：1. Less cleave sites; 2. High specificity； 3. More production.
（1）Proteases cleavage：
1．Trypsin：C-terminal of Arg, Lys. High specificity
2．Chymotrypsin： C-terminal of Phe, Trp, Tyr.
1. Separation of amino acids by ion exchange chromatography
Amino Acid Separation
Unfortunately, amino acids are not colored as described in this overhead. Therefore, what methods would you use to first check if an amino acid is indeed present?
A-E-F-S-G-I-T-P-K
L-V-G-K
• Chymotrypsin Cleavage:
L-V-G-K-A-E-F S-G-I-T-P-K
• Edman degradation: L
• Correct sequence:
L-V-G-K-A-E-F-S-G-I-T-P-K
<2> Enzymatic hydrolysis：
7. Clostripain（Arg protease ）： c-terminal of Arg.
（2）Chemical cleavage：
1．CNBr： c-terminal of Met.
CNBr is useful because proteins usually have only few Met residues.
（1）Proteases cleavage：
1．Trypsin：C-terminal of Arg, Lys. High specificity
2．Chymotrypsin： C-terminal of Phe, Trp, Tyr.
1. Separation of amino acids by ion exchange chromatography
Amino Acid Separation
Unfortunately, amino acids are not colored as described in this overhead. Therefore, what methods would you use to first check if an amino acid is indeed present?
A-E-F-S-G-I-T-P-K
L-V-G-K
• Chymotrypsin Cleavage:
L-V-G-K-A-E-F S-G-I-T-P-K
• Edman degradation: L
• Correct sequence:
L-V-G-K-A-E-F-S-G-I-T-P-K
<2> Enzymatic hydrolysis：
7. Clostripain（Arg protease ）： c-terminal of Arg.
（2）Chemical cleavage：
1．CNBr： c-terminal of Met.
CNBr is useful because proteins usually have only few Met residues.
生物化学绪论 ppt课件
生物化学绪论
生物化学
一、生物化学的定义 生物化学(biochemistry) 是研究生物体内的化 学分子和化学反应的基础生命科学,从分子水平探讨 生命现象的本质，即生命的化学。 二、生物化学与分子生物学发展简史
二、生物化学与分子生物学发展简史
叙述生物化学阶段：18世纪中叶—19世纪末
动态生物化学阶段：20世纪初开始
1994年 生理学或医学奖 lfred G．Gilman（美国）Martin ROdbell（美国），发现 G蛋白及其在细 胞内信号转导中的作用 1993年 生理学或医学奖 Richard J．ROberts（美国）PhilliP A．SharP（美国），发现断裂基因化 学奖 Kary n．Mullis（美国），发明 PCR方法 Michael Smith（加拿大），建立 DNA合成用于定点诱变研究 1992年 生理学或医学奖 Edmond H．Fischer（美国）Edwin G．Krebs（美国），发现可逆蛋白质 磷酸化是一种生物调节机制 1989年 生理学或医学奖 Harold E．Varmus（美国）J．Michael Bishop（美国），发现反转录病毒 癌基因的细胞起源 化学奖 Sidney Altman（美国）Thorn R．Cech（美国），发现 RNA的催化性质 1988年 生理学或医学奖 James W．Black（英国）ertrude B．Elion（美国）Gong H．Hitchings（ 美国），发现“代谢”有关药物处理的重要原则
1964年 生理学或医学奖 Konard Bloch（美国）Feoder Lgnen（德国），发现胆固醇和脂肪酸代 谢的机制和调节 化学奖 Derothy Crowfoot Hodgkin（英国），用 X射线技术测定重要生化物质 的结构 1962年 生理学或医学奖 Francis H．C． Crick（英国）James D．Watson（美国）Maurice H． F． Wilkins（英国），发现核酸的分子结构（DNA双螺旋）及其对于活 性物质中信息转移的重要性 化学奖 Max F．Perutz（英国）JOhn C．Kendrew（英国），关于球状蛋白质 （血红蛋白、肌红蛋白）结构的研究 1959年 生理学或医学奖 Severo Ochoa（美国）Arthur KOrnbefg（美国），发现 RNA和 DNA生 物合成机制
生物化学
一、生物化学的定义 生物化学(biochemistry) 是研究生物体内的化 学分子和化学反应的基础生命科学,从分子水平探讨 生命现象的本质，即生命的化学。 二、生物化学与分子生物学发展简史
二、生物化学与分子生物学发展简史
叙述生物化学阶段：18世纪中叶—19世纪末
动态生物化学阶段：20世纪初开始
1994年 生理学或医学奖 lfred G．Gilman（美国）Martin ROdbell（美国），发现 G蛋白及其在细 胞内信号转导中的作用 1993年 生理学或医学奖 Richard J．ROberts（美国）PhilliP A．SharP（美国），发现断裂基因化 学奖 Kary n．Mullis（美国），发明 PCR方法 Michael Smith（加拿大），建立 DNA合成用于定点诱变研究 1992年 生理学或医学奖 Edmond H．Fischer（美国）Edwin G．Krebs（美国），发现可逆蛋白质 磷酸化是一种生物调节机制 1989年 生理学或医学奖 Harold E．Varmus（美国）J．Michael Bishop（美国），发现反转录病毒 癌基因的细胞起源 化学奖 Sidney Altman（美国）Thorn R．Cech（美国），发现 RNA的催化性质 1988年 生理学或医学奖 James W．Black（英国）ertrude B．Elion（美国）Gong H．Hitchings（ 美国），发现“代谢”有关药物处理的重要原则
1964年 生理学或医学奖 Konard Bloch（美国）Feoder Lgnen（德国），发现胆固醇和脂肪酸代 谢的机制和调节 化学奖 Derothy Crowfoot Hodgkin（英国），用 X射线技术测定重要生化物质 的结构 1962年 生理学或医学奖 Francis H．C． Crick（英国）James D．Watson（美国）Maurice H． F． Wilkins（英国），发现核酸的分子结构（DNA双螺旋）及其对于活 性物质中信息转移的重要性 化学奖 Max F．Perutz（英国）JOhn C．Kendrew（英国），关于球状蛋白质 （血红蛋白、肌红蛋白）结构的研究 1959年 生理学或医学奖 Severo Ochoa（美国）Arthur KOrnbefg（美国），发现 RNA和 DNA生 物合成机制
biochemistry chapter3PPT课件
▲the term proteome is derived from proteins expressed by the genome.
▲The genome tells us what is possible什么是可能的, the proteome tells us what is functionally present什么是(功能上)存在的
4
• ▲e.g. which proteins interact to form a signal-transduction
pathway or an ion channel in a membrane
• ▲the proteome is not a fixed characteristic of the cell. Rather,
complex level of information content, the level of functional information, which encompasses the type, functions, and
interactions of proteins that yield a functional unit. 结构信息层面→功能信息层面(包括作为基本功能单位的蛋白的 类型,功能和相互作用)
2
• How do AA sequences specify the
conformations of proteins?
• How do proteins bind specific substrates and
other molecules, mediate catalysis, and transduce energy and information?结合特异底 物和其它分子,催化反应,转换能量和信息.
▲The genome tells us what is possible什么是可能的, the proteome tells us what is functionally present什么是(功能上)存在的
4
• ▲e.g. which proteins interact to form a signal-transduction
pathway or an ion channel in a membrane
• ▲the proteome is not a fixed characteristic of the cell. Rather,
complex level of information content, the level of functional information, which encompasses the type, functions, and
interactions of proteins that yield a functional unit. 结构信息层面→功能信息层面(包括作为基本功能单位的蛋白的 类型,功能和相互作用)
2
• How do AA sequences specify the
conformations of proteins?
• How do proteins bind specific substrates and
other molecules, mediate catalysis, and transduce energy and information?结合特异底 物和其它分子,催化反应,转换能量和信息.
生物化学英语版
生物化学英语版陈彻席亚明目录Chapter 1 Overview of Cell1.1 Structural Organization of Prokaryotic Cells1.2 Structural Organization of Eukaryotic CellsMembraneCytoskeletonThe NucleusThe Endoplasmic Reticulum and Golgi Apparatus MitochondriaLysosomes and PeroxisomesKey WordsChapter 2 Protein2.1 Amino AcidsGeneral Structures of Amino AcidsStructures of the 20 Common Amino AcidsSpectroscopic Properties of Amino AcidsThe Ninhydrin ReactionIonization of Amino Acids2.2 Structures of ProteinsPeptidePeptide BondsPrimary StructureSecondary StructureSupersecondary StructureTertiary StructureQuaternary StructureThe Classification of Proteins2.3 Structure-function Relationships of ProteinsPrimary Structure Determine the Conformation of Protein Protein Denaturation and RenaturationProtein StabilityCorrelation between Conformation and Function of Protein Protein Misfolding and Diseases2.4 Protein Purification TechniquesSalting OutDialysisGel Filtration ChromatographyIon Exchange ChromatographyAffinity ChromatographyElectrophoresisSDS Polyacrylamide Gel Electrophoresis （SDS-PAGE）Isoelectric FocusingTwo Dimensional ElectrophoresisUltracentrifugationKey WordsChapter 3 Enzymes3.1 The History of Enzymes3.2 Naming and Classification of EnzymesEC 1 OxidoreductasesEC 2 TransferasesEC 3 HydrolasesEC 4 LyasesEC 5 IsomerasesEC 6 Ligases3.3 Structural Components of EnzymesApoenzymes,Cofactors and HoloenzymesActive Center of EnzymesIsozymes3.4 The Properties of Enzymatic CatalysisEnzymes Greatly Accelerate the Rates of Chemical Reactions Specificity of EnzymesControllability of Enzyme Activity3.5 Mechanism of Enzymatic CatalysisTransition State and Activation EnergyLock and Key HypothesisInduced Fit HypothesisEnzyme-Substrate Interactions3.6 Enzyme KineticsSubstrate Concentration Affects the Rate of Reactions Michaelis-Menton KineticsThe Significance of KmMeasurement of Km and VmaxEnzyme Concentration Affects the Rate of Reactions Temperature Affects the Rate of ReactionspH Value Affects the Rate of ReactionsInhibition of Enzyme Catalyzed Reactions……Chapter 4 Coenzymes and VitaminsChapter 5 Nucleic AcidsChapter 6 DNA ReplicationChapter 7 RNA Synthesis-TranscriptionChapter 8 Protein Synthesis-TranslationChapter 9 Regulation of Gene ExpressionChapter 10 Carbohydrate MetabolismChapter 11 Electron Transport and Oxidative Phosphorylation Chapter 12 Lipid MetabolismChapter 13 Amino Acid MetabolismChapter 14 Nucleotides MetabolismChapter 15 Cell SignalingChapter 16 The Popular Techniques in Molecular Biology ReferenceIndex。
生物化学原理课件(英文)：Chapter32 Nucleotide Metabolism
Why does UMP Cure Orotic Aciduria?
Carbamoyl Phosphate
X Orotate UMP Synthetase
Disease (-UMP)
– No UMP/excess orotate
Feedback Inhibition
☺Disease (+UMP)
Purines are synthesized on the Ribose ring
The metabolic origin of the nine atoms in the purine ring system
Many Steps Require an Activated Ribose Sugar (PRPP)
Catalyzes conversion of NDP to dNDP Highly regulated enzyme Regulates the level of cellular dNTPs Activated prior to DNA synthesis Controlled by feedback inhibition
The synthesis of AMP and GMP from IMP
Salvage Pathway for Purines
Hypoxanthine
or
+ PRPP = IMP or GMP + PPi
Guanine
(HGPRTase)
Adenine + PRPP = AMP + PPi
(APRTase)
de novo Pathway
Salvage Pathway
De novo Synthesis Committed step: This is the point of no return
生物化学课件Chapter 3 Amino acids and Peptides
• Later, enzyme digestion of proteins (much milder condition) helped to unveil which of these identified amino acids are actual building blocks of proteins.
DNA replication
Immune response (defending)
Light production (Luciferase)
O2 transport (Hemoglobin)
Support (keratin)
All proteins are constructed from the same set of 20 standard amino acids!
a
Common structure
1.
3.
The 20 amino acids are commonly categorized into five groups based on side chain features.
2. 4.
5.
Each amino acid possesses: 1. a common name 2. a three-letter abbreviation 3. an one-letter symbol
Biochemistry lecture 2 (Sept. 18, 2014)
Part I Structure and Catalysis
Chapter 3 Amino acids and Peptides
By Prof. Zengyi Chang (昌增益）
a-amino acid
Proteins are structurally and
DNA replication
Immune response (defending)
Light production (Luciferase)
O2 transport (Hemoglobin)
Support (keratin)
All proteins are constructed from the same set of 20 standard amino acids!
a
Common structure
1.
3.
The 20 amino acids are commonly categorized into five groups based on side chain features.
2. 4.
5.
Each amino acid possesses: 1. a common name 2. a three-letter abbreviation 3. an one-letter symbol
Biochemistry lecture 2 (Sept. 18, 2014)
Part I Structure and Catalysis
Chapter 3 Amino acids and Peptides
By Prof. Zengyi Chang (昌增益）
a-amino acid
Proteins are structurally and
生物化学-biochemistry ppt课件
5
Foundations of Modern Biochemistry
Goals of biochemistry Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms.
12
Foundations of Modern Biochemistry
The idea of the gene, – a unit of hereditary information, – was first proposed in the mid-nineteenth century by Gregor Mendel.
(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).
8
Note
All living matters usually have the following properties :
living matter: 生物体; in molecular terms: 以分子的观点; at molecular levels: 从分子水平
Foundations of Modern Biochemistry
Goals of biochemistry Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms.
12
Foundations of Modern Biochemistry
The idea of the gene, – a unit of hereditary information, – was first proposed in the mid-nineteenth century by Gregor Mendel.
(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).
8
Note
All living matters usually have the following properties :
living matter: 生物体; in molecular terms: 以分子的观点; at molecular levels: 从分子水平
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(2) Storage and transport of biochemical molecules (Hb, Mb)
(3) Physical cell support and shape (tubulin, actin, collagen)
(4) Mechanical movement (flagella, mitosis, muscles)
➢ (2) According to polymerization of protein molecules;
➢ Monomeric proteins ➢ Oligomeric proteins (multimeric proteins)
➢ (3) According to conjugation of protein molecules;
106 Da or more。 ➢ Usually insulin (5700 Da) or RNase (126000 Da)
was as the boundary of proteins and polypeptides. ➢ Mr of proteins ≈ Mr of amino acid ×110.
➢Mirror image pairs of amino acids are designated L (levo) and D (dextro)
➢Proteins are assembled from L-amino acids (few D-amino acids occur in nature)
Chapter 3 Amino Acids and the Primary
Structures of Proteins
3.1 Outline of Proteins 3.2 Structures of Amino Acids 3.3 Other Amino Acids and Amino
Acid Derivatives 3.4 Ionization of Amino Acids 3.5 Chemical reactions of AAs: 3.6 Peptide Bonds Link Amino Acids
Ball-and-stick model
Perspective
Fischer projections
Fischer projections - horizontal bonds from a
chiral center extend toward the viewer, vertical bonds extend away from the viewer
in Proteins
3.7 Protein Purification Techniques 3.8 Amino Acid Composition of Proteins 3.9 Determining the Sequence of Amino
Acid residues 3.10 Comparisons of the Primary
4. Configuration of amino acids.
Stereochemistry • Stereoisomers - compounds that have the
same molecular formula but differ in the arrangement of atoms in space • Enantiomers - nonsuperimposable mirror images • Chiral carbons - have four different groups attached
A.Aliphatic R groups: B.Aromatic R groups: C.Sulfur-containing R groups: D.Side chains with alcohol groups: E.Basic R groups: F.Acidic R groups and their amide
conformations of the peptide chain, such as a-helices and b-sheets ➢Tertiary structure - describes the shape of the fully folded polypeptide chain ➢Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule
Proline has a nitrogen in the aliphatic ring system
• Proline (Pro, P) - has a three carbon side chain bonded to the a-amino nitrogen
• The heterocyclic pyrrolidine ring restricts the geometry of polypeptides = causes abrupt changes in the direction of the polypeptide chain
Mirror Images of Amino Acid
a
a
Mirror image of Stereoisomers
➢ The 19 chiral amino acids used in the assembly of proteins are all of the L configuration, although a few D-amino acids occur in nature.Why ?
(5) Decoding information in the cell (translation, regulation of gene expression)
(6) Hormones or hormone receptors (growth hormone, insulin receptor)
(7) Other specialized functions (antibodies, toxins etc)
3.2 Structures of Amino Acids
1. General structure of amino acids. More than 200 different AAs are
found in living organisms,including the 20 common (standard) amino acids.
• Proline (Pro, P) 3-carbon chain connects a-C and N = ring structure
Four aliphatic amino acid structures
Important in protein structure and folding since their R groups cluster away from water
COO-
Amino group
+ H3 N
a
Carboxylic group
H
R group
H = Glycine CH3 = Alanine
The R groups are different in 20 AAs.
Zwitterionic form of amino acids
• Under normal cellular conditions amino acids are zwitterions (dipolar ions): Amino group = -NH3+ (Protonated) Carboxyl group = -COO- (Ionized)
derivatives:
A. Aliphatic (hydrophobic) R Groups
• Glycine (Gly, G) - the a-carbon is not chiral since there are two H’s attached (R=H) = smallest and fits easiest into small nitches
5.Classification of the 20 common amino acids
(1).The three-letter and one-letter abbreviations.
(2). Classification of amino acids by chemical construction.
2. Classification of proteins:
(1) According to shape of prlar proteins
Usually water soluble, compact, roughly spherical Hydrophobic interior, hydrophilic surface globular proteins include enzymes, carrier and regulatory proteins
➢ Fibrous proteins
Provide mechanical support – not water soluble Often assembled into large cables or threads α-Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones and teeth
Structures of Proteins Reveal Evolutionary Relationships
3.1 Outline of Proteins
(3) Physical cell support and shape (tubulin, actin, collagen)
(4) Mechanical movement (flagella, mitosis, muscles)
➢ (2) According to polymerization of protein molecules;
➢ Monomeric proteins ➢ Oligomeric proteins (multimeric proteins)
➢ (3) According to conjugation of protein molecules;
106 Da or more。 ➢ Usually insulin (5700 Da) or RNase (126000 Da)
was as the boundary of proteins and polypeptides. ➢ Mr of proteins ≈ Mr of amino acid ×110.
➢Mirror image pairs of amino acids are designated L (levo) and D (dextro)
➢Proteins are assembled from L-amino acids (few D-amino acids occur in nature)
Chapter 3 Amino Acids and the Primary
Structures of Proteins
3.1 Outline of Proteins 3.2 Structures of Amino Acids 3.3 Other Amino Acids and Amino
Acid Derivatives 3.4 Ionization of Amino Acids 3.5 Chemical reactions of AAs: 3.6 Peptide Bonds Link Amino Acids
Ball-and-stick model
Perspective
Fischer projections
Fischer projections - horizontal bonds from a
chiral center extend toward the viewer, vertical bonds extend away from the viewer
in Proteins
3.7 Protein Purification Techniques 3.8 Amino Acid Composition of Proteins 3.9 Determining the Sequence of Amino
Acid residues 3.10 Comparisons of the Primary
4. Configuration of amino acids.
Stereochemistry • Stereoisomers - compounds that have the
same molecular formula but differ in the arrangement of atoms in space • Enantiomers - nonsuperimposable mirror images • Chiral carbons - have four different groups attached
A.Aliphatic R groups: B.Aromatic R groups: C.Sulfur-containing R groups: D.Side chains with alcohol groups: E.Basic R groups: F.Acidic R groups and their amide
conformations of the peptide chain, such as a-helices and b-sheets ➢Tertiary structure - describes the shape of the fully folded polypeptide chain ➢Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule
Proline has a nitrogen in the aliphatic ring system
• Proline (Pro, P) - has a three carbon side chain bonded to the a-amino nitrogen
• The heterocyclic pyrrolidine ring restricts the geometry of polypeptides = causes abrupt changes in the direction of the polypeptide chain
Mirror Images of Amino Acid
a
a
Mirror image of Stereoisomers
➢ The 19 chiral amino acids used in the assembly of proteins are all of the L configuration, although a few D-amino acids occur in nature.Why ?
(5) Decoding information in the cell (translation, regulation of gene expression)
(6) Hormones or hormone receptors (growth hormone, insulin receptor)
(7) Other specialized functions (antibodies, toxins etc)
3.2 Structures of Amino Acids
1. General structure of amino acids. More than 200 different AAs are
found in living organisms,including the 20 common (standard) amino acids.
• Proline (Pro, P) 3-carbon chain connects a-C and N = ring structure
Four aliphatic amino acid structures
Important in protein structure and folding since their R groups cluster away from water
COO-
Amino group
+ H3 N
a
Carboxylic group
H
R group
H = Glycine CH3 = Alanine
The R groups are different in 20 AAs.
Zwitterionic form of amino acids
• Under normal cellular conditions amino acids are zwitterions (dipolar ions): Amino group = -NH3+ (Protonated) Carboxyl group = -COO- (Ionized)
derivatives:
A. Aliphatic (hydrophobic) R Groups
• Glycine (Gly, G) - the a-carbon is not chiral since there are two H’s attached (R=H) = smallest and fits easiest into small nitches
5.Classification of the 20 common amino acids
(1).The three-letter and one-letter abbreviations.
(2). Classification of amino acids by chemical construction.
2. Classification of proteins:
(1) According to shape of prlar proteins
Usually water soluble, compact, roughly spherical Hydrophobic interior, hydrophilic surface globular proteins include enzymes, carrier and regulatory proteins
➢ Fibrous proteins
Provide mechanical support – not water soluble Often assembled into large cables or threads α-Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones and teeth
Structures of Proteins Reveal Evolutionary Relationships
3.1 Outline of Proteins