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課堂講稿


本頁翻譯進度

燈號說明

審定:邱富敏(簡介並寄信)
翻譯:溫榮弘(簡介並寄信)
編輯:汪仁傑(簡介並寄信)

這些摘要提供一個此課程所含括之課題的概要。


介紹

運用生物材料的發展與人類文明進展的相關性。介紹生物材料的分子結構。生物材料的歷史。

水分子特性在決定生物材料結構上的重要性。將討論蛋白質的水合(膠原蛋白與其它的細胞外間質),去氧核糖核酸、糖與其它生物分子。

氨基酸

它們的化學與物理特性。其酸性、鹼性、極性與非極性分子基,以及特定氨基酸的特殊性質。離子強度、酸鹼度…等對氨基酸的溶解度、帶電性與質子化的影響。

螺旋

阿爾發螺旋、310螺旋、π螺旋、卷曲螺旋等等。不同的螺旋是依據二平面夾角與分子基組成來決定。也會介紹螺旋束、雙股卷曲螺旋、三或四股卷曲螺旋、超螺旋。不同富含螺旋的蛋白質結構模型將會用來展現蛋白質螺旋的特性。在生物材料中的阿爾發螺旋,以及阿爾發螺旋結構的設計。

胜肽與蛋白質結構

在氨基酸之間的胜肽鍵特性。胜肽鍵的平面性質及二平面夾角的限制是如何產生特定的次級結構。解釋Ramachandran圖。蛋白質的一級與二級結構。氨基酸序列的組成與形成特定次級結構的傾向之間的相關性。由胜肽序列來預測次級結構。

貝它褶板

反向平行的貝它褶板、平行貝它褶板、貝它褶板扭曲、貝它螺旋等等。富含貝它褶板的蛋白質與貝它褶板的主要序列組成。貝它褶板與富含較高階貝它褶板結構的特性。在不同生物材料中的貝它褶板。

用在分子結構的研究與分析上的工具(I):X光結晶學

X光單晶體繞射、光纖繞射、粉體繞射。概述用來確定生物材料結晶結構的X光結晶學的程序。試體準備、儀器設備、繞射分析的準備,並討論目前的限制。

用在分子結構的研究與分析上的工具(II):核磁共振

高解析度核磁共振分析、溶液型核磁共振與固態型核磁共振。

用在分子結構的研究與分析上的工具(III)

旋光分光儀、雷曼光學、傅立葉轉換紅外線光譜儀、原子力顯微鏡、穿透式電子顯微鏡、掃描式電子顯微鏡、光學散射。描述每一種技術及其所產生的資料型式。探討每一種結構分析工具的應用與限制。

膠原蛋白

膠原蛋白的分子結構。膠原蛋白I-XVIII的主要序列與不同型態的膠原蛋白之間的差異。富含脯氨酸的螺旋、富含氨基乙酸的螺旋,以及這些分子基與水分子在形成膠原蛋白纖維的較高階結構上的重要性。膠原蛋白結構的纖維繞射模式與單晶的膠原蛋白片斷結構。建構膠原蛋白的分子模型在瞭解分子結構上的重要性。其它纖維蛋白質的分子結構。

絲蛋白

蜘蛛絲與蠶絲的分子結構。絲蛋白質的主要序列,以及短胜肽序列重複的重要性。絲心蛋白的基因編碼。蠶絲與蜘蛛絲的一些型態,如牽引絲與補抓絲之間的比較。目前趨向重組絲蛋白或合成絲蛋白的製造與加工的方法。每一隻蠶如何能夠產生超過2公里長的絲蛋白纖維。

角質

角質的分子結構。羊毛、毛髮、羽毛、角、指甲、牛皮、軟毛、鱗、皮膚與其它富含角質的材料之間的差異。藉由它們的主要、次級與較高階結構的組成來確定這些材料的特性。

生物源礦物的分子結構(I)

貝殼、矽藻與珊瑚。生物有機質成礦過程與一般生物產生無機結構的範例。建構生物成礦支架的蛋白質主要序列與結構。所使用到的礦物型態與其結晶如何在材料中組織起來[多3篇論文]。

生物源礦物的分子結構(II)

骨頭與牙齒。骨頭與牙齒在巨觀結構上的差異。形成骨頭與牙齒生物源礦物的分子基礎。這些生物源礦物的分子結構如何轉譯成抗斷裂並具有強度。

生物黏著劑的分子結構

蛋白質如何在有水存在下能很緊密地附著在表面上。能夠製造粘著劑的生物範例,以及這些粘著劑型態上的多樣性。並詳細介紹幾丁質與其它粘著劑。

螢光蛋白質的分子結構

從僧帽水母上所取得的綠色螢光蛋白質是第一種會自發螢光的蛋白質實例。其它螢光蛋白質的來源。綠色螢光蛋白質是如何發螢光?綠色螢光蛋白質的貝它桶狀結構,以及其在製造螢光分子上的重要性。也會討論其它的螢光型態:藍色、黃色與紅色蛋白質。

核酸

去氧核糖核酸與核糖核酸是奈米材料的建構區塊。核酸的物理與化學性質。去氧核糖核酸的雙螺旋結構與其類別。混合能量與互補性在引導去氧核糖核酸/核糖核酸結構組合時的重要性。合成與操作用的工具,以及去氧核糖核酸或核糖核酸的研究。

脂質

作為生物材料的脂質。分子結構與性質。磷脂質分子如何組織並組合成細胞膜、微膠粒、細胞小管等。脂質的合成與功能性。

醣類

醣類基生物材料的分子結構。六碳糖與五碳糖的結構,以及糖鏈。細胞膜質與相關材料的較高階結構,以及這些材料的性質。由碳水化合物組成的生物材料。

生物擬態與設計

由自然界所啟發的生物材料分子設計與工程。新型支架、新型生物源礦物、新型黏著劑、新型螢光材料。以生物擬態做為從生物材料創造具有變化或新穎功能的典範。自我組裝、分子對位與交互鏈結在從奈米級建構區塊建構出巨型生物材料細絲上的重要性。

自我組裝胜肽系統

短的自我組裝胜肽序列的合理設計。組裝結構的物理性質與結構特性。這些系統在生醫工程、生物工程研究與奈米科技上的應用。

其它自我組裝的胜肽與蛋白質系統

從A. Aggeli,A. Belcher,C. Dobson,R. Ghadiri,M. Hecht,J. Kelly,S. Lindquist,S. Stupp,D. Tirrell而來的一些例子。

去氧核糖核酸分子機械與構裝

射頻生物學、去氧核糖核酸奈米晶體有機體、去氧核糖核酸奈米線…等等。

再生醫學

運用在組織工程上的生物材料之進展狀況與對社會的衝擊。組織工程超群的未來。

生物運算

運用生物材料做為資訊處理與運算的最近進展。運用生物材料在運算上的未來發展。




These summaries provide an overview of the topics covered in this course.


Introduction

The correlation of developments in use of biological materials with the advancement of human civilization. Introduction to the molecular structure of biological materials. History of biological materials.

Water

The importance of the properties of the water molecule in determining the structure of biological materials. Hydration of proteins (collagens and other ECMs), DNA, sugars and other biological molecules discussed.

Amino Acids

Their chemical and physical properties. Acidic, basic, polar, and nonpolar residues, and special properties of specific amino acids. Influence of ionic strength, pH, etc. on the solubility, charge, and protonation of amino acids.

Helices

Alpha helices, 310 helix, pi helix, coiled-coils, etc. Variation of helices based on dihedral angels and residue composition. Helical bundles, two strand coiled-coils, three or four strand coiled-coils, supercoils will be described. Various helical rich protein structure models will be used to reveal the properties of protein helices. Alpha helices in biological materials, and design of alpha-helical structures.

Peptide and Protein Structure

Characteristics of the peptide bond between amino acids. How the planar nature of the peptide bond and restrictions on the dihedral angles produce specific secondary structures. Explanation of the Ramachandran plot. Primary and secondary structures of proteins. The relationship between the composition of amino acid sequence and the propensity to form specific secondary structures. Prediction of secondary structure from peptide sequence.

Beta-Sheets

Antiparallel beta-sheet, parallel beta-sheets, beta-sheet twist, betahelices, etc. Beta-sheet rich proteins and primary sequence composition of betasheets. Properties of the beta-sheet and higher order beta-sheet rich structures. Beta-sheets in various biological materials.

Tools Used in Study and Analyses of Molecular Structures (I): X-Ray Crystallography

X-ray single crystal diffraction, fiber diffraction, powder diffraction. Outline the process of X-ray crystallography for determination of the crystal structure of biological materials: Preparation of the samples, instrumentation, diffraction analyses, and discussion of the current limitations.

Tools Used in Study and Analyses of Molecular Structures (II): Nuclear Magnetic Resonance (NMR)

High resolution NMR analyses, Solution NMR and solid state NMR.

Tools Used in Study and Analyses of Molecular Structures (III)

Circular Dichroism, Raman, FTIR, AFM, TEM, SEM, light scattering, Description of each technology and type of data generated. Discussion of the applications and limitations of each structure analysis tool.

Collagen

Molecular structure of collagen. Primary sequences of collagen I-XVIII and differences between the various types of collagen. The proline rich helix, glycine rich helix, and importance of these residues and water molecules in forming the higher order structure of collagen fibers. The fiber diffraction pattern of the collagen structure and single crystal collagen fragment structure. The importance of building the molecular model of collagen in the understanding of molecular structures. Molecular structure of other fibrous proteins.

Silk

Molecular structure of spider and silkworm silk. The silk protein primary sequences, and the significance of short peptide sequence repeats. The correlation of beta-sheet content with the strength, flexibility, and elasticity of silks. The genetic encoding of the silk fibroin. Several types of spider silk, i.e. dragline silk and capture silk, and silkworm silk are compared. Current approaches to the production and processing of recombinant or synthetic silks. How each silk worm produces over 2 km long silk fiber.

Keratin

Molecular structure of keratin. The differences between wool, hair, feather, horn, nail, cowhide, fur, scale, skin and other keratin rich materials. The properties of these materials as determined by their primary, secondary, and higher order structure compositions.

Molecular Structure of Biominerals (I)

Seashells, diatoms and corals. The biomineralization process and general paradigms for biology creating inorganic structures. The primary sequences and structures of proteins that build the scaffolds for biomineralization. The types of minerals used and how the crystals are organized in the materials. [ + 3 papers]

Molecular Structure of Biominerals (II)

Bone and tooth. Differences in macrostructures of bones and teeth. Molecular basis for formation of bone and teeth biominerals. How the molecular structure of these biomaterials translates to fracture resistance and strength.

Molecular Structure of Biological Adhesives

How the proteins adhere tightly on surfaces in the presence of water. Examples of organisms that produce adhesives and the diversity in types of adhesives. Chitin and others are described in detail.

Molecular Structure of Fluorescent Proteins

Green fluorescent protein (GFP) from the Aequorea jellyfish as the first example of an autonomously fluorescent protein. Origin of other fluorescent proteins. How is GFP fluorescent? The beta-barrel structure of GFP and significance in creating a fluorescent molecule. Other fluorescent variants are discussed: blue, yellow and red proteins.

Nucleic Acids

DNA and RNA as building blocks for nanomaterials. Physical and chemical properties of the nucleic acids. Double helical structure of DNA and types of DNA helices. Importance of hybridization energy and complementarity in directing assembly of DNA/RNA structures. Tools for synthesis, manipulation, and study of DNA or RNA.

Lipids

Lipids as biomaterials. Molecular structure and properties. Organization and assembly of phospholipid molecules into membranes, micelles, tubules, etc. Synthesis and functionalization of lipids.

Saccharides

Molecular structure of saccharide-based biological materials. Structures of hexose and pentose sugars and glycosidic bonds. Higher order structure of cellulose and related materials, and properties of such materials. Biological materials composed of carbohydrates.

Biomimicry and Design

Molecular design and engineering of biological materials inspired by nature. New scaffolds, new biominerals, new adhesives, new fluorescent materials. Biomimicry as a paradigm for creating molecules with modified or novel functions from biomaterials. The importance of self-assembly, molecular alignment, and cross-linking in the construction of macroscale biological material filaments from nano-scale building blocks.

Self-Assembling Peptide Systems

Rational design of short self-assembling peptide sequences. Physical properties and structural features of assembled structures. Applications of such systems in biomedical engineering, biological engineering research and nanotechnology.

Other Self-Assembling Peptide and Protein Systems

Examples from A. Aggeli, A. Belcher, C. Dobson, R. Ghadiri, M. Hecht, J. Kelly, S. Lindquist, S. Stupp, D. Tirrell

DNA Molecular Machines and Assembly

Radio Frequency Biology (RF biology), DNA nanocrystal organization, DNA wires, etc.

Regenerative Medicine

Perspective of advancement in biological materials used in tissue engineering and the impact to society. The bionic future of tissue engineering.

Biocomputing

Recent advances in using biological materials for information processing and computing. Perspectives on use of biological materials in computing.




 
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