糖生物学要点.4- 学习指南

学习指南

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第1章 历史背景与概述

1. 哪些因素阻碍了聚糖生物学（“糖生物学”）研究与传统分子和细胞生物学的整合？
2. 为什么进化反复选择聚糖作为所有细胞表面的主要分子？
3. 解释细胞外聚糖和核/胞质聚糖之间的区别。
4. 影响细胞表面和分泌分子上的聚糖组成和结构的各种因素有哪些？
5. 讨论聚糖参与关键细胞内功能的各种方式。

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第2章 单糖多样性

1. 脊椎动物聚糖中最常见的九种单糖是什么？
2. 定义以下术语：D-和L-立体化学、差向异构体和异构体、轴向和赤道、还原端和非还原端以及α和β连接。
3. 葡萄糖的α-糖苷将糖苷基定位在轴向，而唾液酸的α-糖苷将这一基团定位在赤道方向。通过将α和β异构体立体化学的定义应用于这两种单糖来解释这种明显的差异。
4. 在自然界中，D-半乳糖只需两个酶促步骤即可转化为L-半乳糖。使用费休投影，显示可以完成这一两步互转化的化学转化。
5. 基于单糖中的原子和官能团，描述它们可能与蛋白质相互作用的方式（例如，静电相互作用、氢键、范德华力和疏水相互作用）。

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第3章 低聚糖和多糖

1. 如果真核生物中有21种氨基酸，只有10种主要单糖，为什么六糖中的单糖组合比六肽中的氨基酸多得多？
2. 什么氨基酸作为N-连接低聚糖的苷元？
3. 硫酸软骨素的重复单位是什么？
4. 硫酸乙酰肝素的柔韧性，而不是硫酸软骨素的柔韧性，哪些独特的结构特征有助于？
5. 命名三种用作抗原的细菌多糖。

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第4章 糖基化的细胞组织

1. 考虑拓扑抑制糖基化对ER/高尔基体隔室的优缺点。
2. 聚糖修饰酶的物理定位和功能定位有什么区别？
3. 描述决定转移酶高尔基体定位的机制。
4. 解释转移酶的定位如何影响细胞表面和分泌分子的聚糖组成。
5. 提出由膜结合酶产生的分泌可溶性糖基转移酶或磺基转移酶的功能。

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第5章 糖基化前体

1. “必需”单糖被定义为生物体无法从头制造的单糖。哺乳动物中是否存在必需的单糖？
2. 为什么动物在饮食中通常不需要甘露糖、岩藻糖或半乳糖？在什么情况下，个人需要膳食补充这些糖中的任何一种？
3. 为什么ER和高尔基体膜需要核苷酸糖转运蛋白？核苷酸糖转运蛋白先天性突变的结果可能是什么？
4. 为什么人类不能代谢纤维素作为能量来源？奶牛和其他反刍动物如何代谢纤维素？
5. 多糖基转移酶复合物可能存在于高尔基体中。这种多酶复合物如何影响聚糖合成？

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第6章 糖基转移酶和聚糖加工酶

1. 解释糖基转移酶如何实现严格的供体底物特异性。
2. 糖基转移酶和糖苷酶已被分配到CAZy数据库中的家族。分配到特定家庭的依据是什么？
3. 举一个糖基转移酶的例子，该酶识别具有特定肽序列基序或蛋白质结构域的受体底物。解释为什么这种糖基转移酶可能已经进化到具有这种受体特异性。
4. 术语“反转”和“保留”在用于描述糖苷酶或糖基转移酶时是什么意思？从机制上讲，我们对反转糖基转移酶如何催化其反应了解多少？
5. 为什么 Km糖基转移酶，对于其供体和受体底物，是确定细胞产生哪些聚糖结构的重要参数？

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第7章 聚糖的生物学功能

1. 聚糖介导或调节生物学功能有哪些不同方式？
2. 解释聚糖的内在功能和外在功能之间的区别。
3. 为什么改变培养细胞和完整动物糖基化的生物学后果如此多变？
4. 鉴于糖基化在种内和种间的差异，如何缩小关键功能的范围？
5. 为什么有些聚糖在经过基因鉴定时可能没有特定的功能？

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第8章 糖生物学的基因组学观点

1. 什么是基于序列的糖基转移酶分类？
2. 描述基因序列预测或无法预测转移酶、水解酶和聚糖结合蛋白功能的方式。
3. 举例说明参与糖基化的双功能酶。提出双功能转移酶进化的驱动力。
4. 根据其基因组中糖苷酶和糖基转移酶基因的相对数量，您可以了解生物体（“生态学”）的生活方式吗？
5. 生物体如何有效地增加其可支配的糖苷酶和糖基转移酶的数量？

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第9章 N-甘氨酸

1. 糖蛋白具有大量N-糖基化位点有哪些优势？
2. 考虑N-糖基化的拓扑结构，并为分离人的形成提供可能的解释5GlcNAc2-Dol 从 Glc 的形成3男人9GlcNAc2-多尔。
3. N-糖生物合成在酵母、无脊椎动物、植物和哺乳动物中有何不同？
4. 什么是N-糖微异质性？N-糖微异质性有哪些优势？
5. 描述N-糖的支化如何调节生长因子信号传导。

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第10章 邻-半乳糖

1. 决定细胞O-GalNAc聚糖组成的因素有哪些？
2. 哪些特性使多肽成为O-GalNAc糖基化的良好受体？您能根据这些特征预测O-GalNAc糖基化位点吗？
3. O-GalNAc聚糖的组装与N-糖的组装有何不同？
4. 解释典型分泌粘蛋白最重要的功能特征。
5. 拥有这么多多肽-N-乙酰半乳糖胺基转移酶有什么优点？

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第11章 鞘糖脂

1. 鞘糖脂的脂质部分神经酰胺赋予它们在膜平面上的自缔合特性。解释原因。
2. 鞘糖脂通过顺式调节和反式识别发挥作用。解释这些术语并提供每个术语的示例。
3. 一些人类和实验动物在负责葡萄糖神经酰胺分解的酶中发生突变，患有脱水。解释原因。
4. 几种人类溶酶体贮积病是由负责鞘糖脂分解的酶突变引起的，导致未切割底物的毒性积聚。即使存在充足的酶，有时也会发生类似的鞘糖脂积聚。解释原因。
5. 与其他聚糖类别相比，动物大脑富含鞘糖脂。描述脑鞘糖脂的两种不同的结构类别及其生理功能的两个示例。

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第12章 糖基磷脂酰肌醇锚

1. GSL 和 GPI 锚点有什么共同点？它们有何不同？
2. 描述具有跨膜结构域的蛋白质与具有GPI锚的蛋白质的行为差异。
3. 解释GPI锚定蛋白如何促进穿过质膜的信号转导。
4. 设计一种测定方法来测量 GPI 锚定中间体在 ER 膜上的分布以及翻转中间体在 ER 上的机制。
5. 为什么糖基磷脂酰肌醇生物合成缺陷引起的疾病的临床症状如此多变？
6. 布氏锥虫或酵母的GPI生物合成途径与人类有何不同？阐明这些差异对我们理解和操纵GPI途径有什么影响？

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第13章 其他种类的真核聚糖

1. 提出一种机制，可以解释改变Notch的糖基化如何影响不同Notch配体的结合。
2. 为什么你认为像ADAMTS13这样具有八个串联TSR的蛋白质需要POFUT2才能正确折叠？
3. 与更简单的O-甘露糖聚糖相比，O-甘露糖基质聚糖在α-肌萎缩聚糖上有什么优势？
4. 胶原蛋白的O-糖基化对其折叠和/或结构有什么影响？
5. C-甘露糖基化色氨酸首先在人尿中检测到。解释为什么这种氨基酸糖苷被排泄到尿液中，而不是作为游离色氨酸和甘露糖。

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第14章 不同聚糖共有的结构

1. 为ABO血型系统中观察到的等位基因变异提出一个函数。非灵长类动物不表达ABO位点——这对你的答案有什么影响？
2. 超急性（移植物）排斥反应 （HAR） 发生在将非人类供体的器官移植到人类中后，由循环抗 Galα1-3Gal 抗体与移植组织的即时反应引起。建议修改供体或受体的方法，以防止 HAR。
3. 比较和对比“LacNAc”和“LacdiNAc”单位。这些末端二糖的存在如何影响唾液酸和岩藻糖的添加？
4. 根据您对卵泡刺激素和促卵泡素的末端结构的了解，提出几种基于聚糖的机制，这些机制可以解释人类不孕症。
5. 某些大肠杆菌菌株与P血型抗原结合并引起尿路感染。保留产生有害聚糖的转移酶可能存在哪些进化优势？

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第15章 唾液酸和其他非尿酸

1. 比较和对比唾液酸与其他单糖的结构。
2. 唾液酸多样性在脊椎动物系统中具有哪些优势？
3. 与其他单糖相比，唾液酸生物合成途径有哪些独特之处？
4. 您如何确定以前未研究的生物体是否含有唾液酸？
5. 对比将α2-6-连接的唾液酸添加到O-GalNAc聚糖和N-聚糖中，以及它们被唾液酸结合凝集素识别。

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第16章 透明质酸

1. 为什么小分子很容易通过高分子量透明质酸（HA）溶液（如眼睛的玻璃体）扩散，而较大的大分子（例如某些蛋白质）则不会？
2. 影响通过HA溶液扩散速率的主要物理和分子因素有哪些，在纯HA基质或仅由部分HA组成的异质细胞外基质中，速率有何不同？
3. HA溶液具有不寻常的粘弹性;例如，HA的作用类似于凝胶，但它可以起到润滑剂的作用。您如何根据链的分子结构来解释这些性质？
4. 为什么HA结合蛋白被认为是凝集素，而与硫酸化糖胺聚糖结合的蛋白质却不是？这两类聚糖结合蛋白有何不同？
5. 与高分子量HA相比，细胞表面HA受体（例如CD44）对6-10个糖单位的HA寡糖的反应如何不同？为什么需要通过相同的受体引发不同的反应？
6. 您将如何证明 HA 链是从还原端还是非还原端组装？
7. 您将如何在体内或细胞环境中证明新的假定透明质酸酶家族成员的透明质酸酶活性？具体来说，如果HA降解发生在细胞内，如何区分HA降解和HA清除？
8. 高分子量 HA 已被证明在肺部病理学中具有组织保护作用，但高分子量 HA 的存在也会阻碍肺功能。如何调和这些观察结果？有没有办法克服HA的这些对比影响，以便它可以有效地用作治疗药物？

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第17章 蛋白聚糖和硫酸化糖胺聚糖

1. 哪些因素会影响细胞中硫酸化糖胺聚糖的精细结构？
2. Ext2（是硫酸乙酰肝素共聚酶复合物的一部分）的过表达增加了链的硫酸化程度。对此发现提供解释。
3. 比较和对比GPI锚定蛋白聚糖与包含跨膜结构域的蛋白聚糖的生物学功能。
4. 举例说明改变细胞和动物中糖胺聚糖代谢的方法。
5. 基于糖胺聚糖-蛋白质相互作用生成药物有哪些选择？

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第18章 核胞质糖基化

1. 您需要什么生化标准来证明聚糖与特定核蛋白或细胞质蛋白的附着？
2. 哪些传统的糖基化途径在膜的细胞质侧发生步骤，可能是核细胞质聚糖的来源？
3. 比较和对比粘蛋白、蛋白聚糖、Notch、糖生成素和 Skp1 的起始糖基化反应。
4. 您将如何证明细胞核中糖胺聚糖的存在？
5. 举例说明糖缀合物最初在细胞质中形成，但后来转运到细胞表面或细胞外空间并发挥作用。

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第19章 O-GlcNAc的修改

1. O-GlcNAc现在已知是细胞中最常见的糖基化形式。为什么花了这么长时间才意识到这一事实？它的发现涉及什么偶然性？
2. O-GlcNAc被认为与磷酸化竞争核蛋白或细胞质糖蛋白上相同或相似的位点。O-GlcNA酰化和磷酸化之间有什么异同？
3. O-GlcNAc糖基化和细胞表面糖基化之间的机理差异是什么？
4. O-GlcNAc如何充当“代谢传感器”？
5. 推测O-GlcNAc如何导致糖尿病的“葡萄糖毒性”。

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第20章 聚糖多样性的进化

1. 哪些过程可以维持群体内的聚糖基因多态性（即结构异质性）？
2. 唾液酸生物学在人类进化过程中发生了哪些变化？
3. 是否有可能通过检查系统发育中的聚糖组成来预测聚糖功能？
4. 使用“比较糖生物学”来确定进化关系（系统发育）存在哪些问题？
5. 哪些糖基化途径支持真核生物的共同起源？

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第21章 真细菌

1. 植物、细菌和酵母都具有提供渗透压抵抗力的细胞壁。比较这些障碍的组成和体系结构。
2. 细菌和动物细胞都利用聚异戊二烯来组装聚糖。比较和对比这些脂质中间体。
3. 比较脂多糖与甘油脂和神经节苷脂的结构。
4. 革兰氏阴性细菌的细胞壁生物合成需要肽聚糖和LPS的协调合成。提出确保体内平衡的潜在监管机制。
5. 比较分枝杆菌和革兰氏阴性细胞壁的结构。

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第22章 古生物

1. 比较和对比古菌、细菌和真核生物中糖蛋白 N-糖基化的途径。
2. 所有细胞都产生酸性聚糖，但负电荷的来源各不相同。大肠杆菌、古菌、酵母和动物细胞中存在的聚糖上的酸性基团是什么？
3. 将古菌中的S层与真核细胞中的表面糖蛋白进行比较。
4. 在真核生物的细胞外基质和古菌细胞壁中寻找分子相似性。
5. 比较细菌穆雷因和古细菌假穆雷因。

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第二十三章 真菌

1. 比较酵母细胞壁的组成和结构以及革兰氏阴性细菌的包膜。
2. 在产生较少β-葡聚糖的突变体中，酵母细胞壁可能发生哪些变化？异常细胞壁可能对这种突变体的形状、生长或活力产生什么影响？
3. 比较和对比酵母和哺乳动物中的N-糖合成。差异的功能意义是什么？
4. 描述真菌中GPI连接蛋白的独特特征。这个过程如何改变这些生物体中的蛋白质定位？
5. 一家制药公司聘请您评估聚糖合成作为药物开发的靶标，以对抗新描述的高毒力致病真菌。描述一组合理的目标和您需要考虑的一些重要问题。

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第24章 植物科和藻类

1. 为什么不表达动物细胞中存在的糖（例如唾液酸）的植物具有与含有这些糖的聚糖结合的凝集素？
2. 植物中的果胶有时与动物中的糖胺聚糖进行比较。它们有何不同？它们有何相似之处？
3. 为什么植物中产生的重组哺乳动物糖蛋白具有免疫原性？
4. 比较植物中甘油脂，细菌中的脂质A和动物中的鞘糖脂的结构。
5. 诱发因子和Nod因子在非常低的浓度下具有活性，因此可以预测它们对其信号转导受体的亲和力将非常高（在pM范围内）。根据您对其他聚糖结合蛋白的了解，如何实现如此高的亲和力？

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第25章 线虫

1. 提出一些进化力量，驱动秀丽隐杆线虫中某些糖基转移酶家族（例如岩藻糖基转移酶）与其他（例如甘露糖基转移酶）相比的大量扩增。
2. 比较和对比秀丽隐杆线虫和脊椎动物中软骨素蛋白多糖的合成。
3. 您将如何选择在N-聚糖形成中存在缺陷的秀丽隐杆线虫突变体？
4. 与脊椎动物系统相比，O-GlcNAc添加到核蛋白和细胞质蛋白中是可有可无的。您如何解释这一发现？
5. 鉴于秀丽隐杆线虫中不含唾液酸，您可以预测秀丽隐杆线虫中聚糖结合蛋白的类型和特异性？

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第26章 节肢动物

1. 比较和对比果蝇、秀丽隐杆线虫和脊椎动物中第一个附着在 N-糖甘露糖核心上的第 N-乙酰葡糖胺残基会发生什么。
2. 比较果蝇缺口的O-糖修饰与脊椎动物缺口EGF重复序列的结构差异。为什么果蝇中的Notch糖基化不如脊椎动物复杂？
3. 将果蝇中鞘糖脂的核心结构与秀丽隐杆线虫和脊椎动物中存在的糖脂进行比较。外链有何不同？
4. β1-4半乳糖基转移酶的转基因表达替代蛋头（egh），蛋头是一种甘露糖基转移酶。关于果蝇鞘糖脂中存在的聚糖的功能，这告诉您什么？
5. 解释dally（一种glypican同源物）的过表达或删除如何减少形态原（如dpp）的扩散。

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第27章 申命记

1. 在研究受精过程中介导精子 - 卵子相互作用的糖蛋白时，为什么使用几种模式动物很重要？
2. 如果您是酶学家，您将如何研究岩藻糖硫酸盐聚合物的合成？
3. 硫酸化fucans也是哺乳动物系统中凝血和炎症的极强抑制剂。基于其结构与其他生物活性聚糖的相似性，提出该作用的机制。
4. 为什么实验室小鼠中一些与聚糖相关的基因敲除没有明显的表型？
5. 如果你在人类中发现了一种新的聚糖，你会选择哪种模式生物进行进一步的研究，你将如何从基因上操纵它？

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第28章 聚糖结合蛋白的发现与分类

1. 如何区分硫酸化糖胺聚糖结合蛋白与凝集素？
2. 假设您发现了一种新的聚糖结合蛋白。您如何确定其分类？
3. 比较和对比可溶性和膜结合凝集素的功能。
4. 对比动物凝集素识别自身和非自身聚糖的功能。
5. 比较具有良好注释的全基因组的生物体中表征聚糖结合蛋白的方法与来自没有全基因组序列的生物体的方法。

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第29章 聚糖识别原理

1. 什么决定了聚糖对GBP的亲和力？
2. 许多类型的蛋白质-聚糖相互作用是低亲和力的，在某些情况下，通过聚集受体和配体来实现高亲和力。通过多价实现高亲和力相互作用的优缺点是什么？
3. 聚糖配体的密度如何影响GBP的结合？这在体内相关吗？
4. 提供与高丰度聚糖结合的相对低亲和力的GBPs，以及与稀缺聚糖结合相对较高的GBP的例子。
5. 为了测量GBP与聚糖的结合动力学和/或亲和力，有几种技术，包括等温滴定量热法和表面等离子体共振法。选择这些或其他技术之一并设计一个实验来测量K一个结合，假设聚糖易于衍生化，如果需要，在其还原端。

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第30章 聚糖识别的结构生物学

1. 霍乱毒素以高亲和力与神经节苷脂GM1结合（Kd∼ 0.1 nm）相对于许多其他GBP与其配体的结合（表现出Kd值在 0.1 μm 至 0.1 mm 范围内）。你如何解释这一观察结果？
2. 列举四种在碳水化合物识别中很重要的分子相互作用。
3. 哪些氨基酸残基可能在结合高硫酸化糖胺聚糖中发挥重要作用？
4. 哪种核磁共振实验可以返回蛋白质结合状态下存在的聚糖几何形状信息？
5. 命名一个数据库，您可以在其中找到 GBP 的结构。

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第31章 R型凝集素

1. 描述蓖麻凝集素-I和蓖麻毒素之间的异同。
2. 为了使蓖麻毒素和其他核糖体失活毒素杀死细胞，它们必须首先进入细胞质。这是怎么发生的？您将如何利用这种机制将货物运送到单元中的不同地点？
3. 解释对一种有毒凝集素产生抗药性的细胞如何对另一种有毒凝集素敏感。
4. 在糖基转移酶和糖苷酶等酶中发现的R型凝集素结构域的功能是什么？
5. 描述细胞中动物凝集素的例子，这些凝集素在顺式和反式拓扑中都与聚糖配体结合。

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第32章 L型凝集素

1. 描述豆科植物种子中存在的L型植物凝集素的可能功能。
2. 如果L型凝集素参与防御，为什么每株植物只产生非常有限的凝集素？
3. 为什么参与蛋白质质量控制的植物种子凝集素和GBP都被归类为L型凝集素？
4. 比较和对比 L 型凝集素中的“果冻卷”折叠、C 型凝集素折叠和链接模块。
5. 植物凝集素通常是糖蛋白，因此通过ER /高尔基体分泌途径成熟。提出一种机制来防止它们在组装和分泌过程中与其他高尔基体糖蛋白相互作用。

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第33章 P型凝集素

1. 为什么使用双标记底物供体很重要[β-32P]UDP[3H]GlcNAc在Man-6-P识别标记物生物合成研究中的应用？
2. 比较和对比通过形成 GlcNAc-P-Man 并随后去除 N-乙酰葡糖胺部分与甘露糖特异性 ATP 依赖性激酶在溶酶体酶上组装 Man-6-P 识别标记的过程。
3. Man-6-P识别标记物主要通过GlcNAc-P-转移酶选择性识别底物蛋白中的肽决定簇在溶酶体酶上组装。描述糖蛋白亚群上聚糖选择性修饰的其他示例。识别决定因素有何不同？
4. 溶酶体酶上的N-糖数量如何影响其对Man-6-P受体之一的亲和力？
5. 比较和对比 Man-6-P 受体在反式高尔基体网络与细胞表面将 Man-<>-P 受体包装成网格蛋白包被的囊泡载体。

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第34章 C型凝集素

1. 许多含有C型凝集素结构域的蛋白质不结合聚糖，而那些结合聚糖的蛋白质称为C型凝集素。区分这两类蛋白质的结构有什么区别？
2. 为什么很难预测C型凝集素将结合的聚糖类型？
3. 一些C型凝集素可以形成低聚物，这大大增加了与聚糖配体相互作用的亲和力。解释寡聚化如何影响相互作用的特异性。
4. 一些C型凝集素，特别是选择素，与某些糖蛋白的结合比与同一细胞上的其他糖蛋白的亲和力更高，即使几种糖蛋白可能表现出相似的聚糖结构。考虑赋予这种优惠约束力的机制。
5. 比较P-选择素与PSGL-1的相互作用与植物凝集素与PSGL-1的结合。

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第35章 I型凝集素

1. 现在已知有十几种人类Siglecs。为什么这些和其他唾液酸结合蛋白直到最近才被发现？
2. 将具有细胞质尾部抑制基序的Siglecs的潜在功能与可以招募激活基序的Siglecs的潜在功能进行比较。
3. 为什么Siglec同源物主要存在于“高等”动物中？
4. 解释一些Siglecs快速进化的可能机制和驱动力。
5. 为什么不表达唾液酸的植物和无脊椎动物具有唾液酸结合蛋白？

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第36章 半乳糖凝集素

1. 您如何解释半乳糖凝集素通常不会在体液中大量发现的发现，即使它们中的大多数是可溶性蛋白质并且经常在细胞外发现？
2. 为什么聚糖支化途径和唾液酸化的变化有可能影响半乳糖凝集素的功能？
3. 半乳糖凝集素如何实现与细胞表面聚糖的高亲和力结合？半乳糖凝集素如何与细胞表面聚糖形成晶格？
4. 解释半乳糖凝集素作为先天免疫效应物如何作为对抗微生物感染的受体。
5. 半乳糖凝集素与多种细胞结合，并在不同的细胞类型中触发各种反应。半乳糖凝集素如何通过细胞表面受体发送信号？

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第37章 微生物凝集素：血凝素、粘附素和毒素

1. 哪些类型的细胞质糖基化事件与感染和病理有关？
2. 将细菌和病毒粘附素的碳水化合物识别域与动物和植物凝集素的碳水化合物识别域进行比较。
3. 除单糖外，还有哪些药剂可用于微生物疾病的抗粘连治疗？
4. 限制抗生素使用的一个严重问题是耐药细菌的迅速出现。这在多大程度上也会成为抗粘连治疗的问题？
5. 多价糖和多价糖是比简单的单体糖更强大的微生物凝集素抑制剂。解释这种现象的原因并讨论其应用。

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第38章 结合硫酸化糖胺聚糖的蛋白质

1. 与硫酸化糖胺聚糖（GAG）结合的蛋白质不被视为凝集素。为什么？
2. 肝素的修饰程度远大于硫酸乙酰肝素。这将如何影响GAG结合蛋白的构象和相互作用？
3. 有助于GAG-蛋白质相互作用的主要键合力类型有哪些？
4. 蛋白质和硫酸化糖胺聚糖之间的相互作用在各种生理和病理生理环境中很重要。它们是特定的吗？
5. 解释HS如何在促进抗凝血酶-凝血酶相互作用和FGF-FGFR相互作用方面发挥类似作用？

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第39章 糖蛋白质量控制中的聚糖

1. 蛋白质结合聚糖在蛋白质折叠和质量控制中充当信号分子的先决条件是什么？
2. 描述急诊室中存在的伴侣类型。
3. 葡萄糖残基的添加和去除是监测蛋白质折叠的质量控制系统的一部分。甘露糖修剪的作用是什么？
4. ER应激反应（ERAD）如何与N-糖合成协调？
5. 比较ER和高尔基体中N-糖的加工与溶酶体和细胞质中N-糖的降解途径。

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第40章 游离寡糖作为生物活性分子

1. 使用来自宿主生物的聚糖作为危险信号有什么优势？
2. 聚糖如何介导非聚糖信号与其受体之间的相互作用？
3. 您能想到宿主免疫系统使用聚糖作为病原体相关分子模式（PAMP）的缺点吗？
4. 通用甲壳素低聚糖的哪些结构修饰 Nod 因子在细菌-植物相互作用中提供了宿主特异性，从而导致豆科植物根瘤形成和固氮？
5. 您如何解释不同的β葡聚糖通过不同的PRR触发植物免疫系统的观察结果？

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第41章 聚糖在全身生理学中的应用

1. 如果聚糖在全身生理学的几乎每个方面都有作用，为什么在某些情况下糖基转移酶的丢失和随后的聚糖结构改变对发育或生理学没有明显的影响？
2. 解释支持聚糖和GBP参与免疫反应的观点的证据。
3. 差异糖基化如何调节糖蛋白的血浆半衰期，这些糖蛋白在哪里清除？
4. 不同上皮表面粘蛋白上的聚糖有哪些不同功能？
5. 聚糖如何调节神经元的生长和修复？

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第42章 细菌和病毒感染

1. 细菌如何通过在其表面涂上多糖胶囊而受益？
2. 致病菌最初是如何定植组织的？
3. 缺乏Toll样受体4的小鼠对细菌感染的敏感性更高还是更低？脂多糖诱导的脓毒症的易感性如何？
4. 流感和单纯疱疹病毒如何与宿主细胞表面接触以引发感染？
5. 可以操纵聚糖来预防或治疗微生物感染吗？

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第43章 寄生虫感染

1. 解释糖结合物在通常与疟疾发病机制相关的高热中的作用。
2. 非洲锥虫在被采采蝇叮咬接种后如何避免免疫系统破坏？
3. 原生动物寄生虫利什曼原虫在传播过程中附着并最终从其白蛉媒介中肠分离的机制是什么？
4. 由寄生虫曼氏血吸虫产生的许多聚糖在受感染宿主中具有高度抗原性。这些聚糖的什么特性使它们如此抗原，这是否提供了制造疫苗的可能性？
5. 哪些糖基转移酶和糖/核苷酸糖转运蛋白可能是寄生虫独有的，因此是化疗干预的潜在靶标？

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第44章 聚糖降解的遗传性疾病

1. 预测如果β-半乳糖苷酶改变，哪些聚糖和组织/器官受到的影响最大。
2. 在溶酶体贮积症中，未降解或部分降解的聚糖和糖肽经常通过尿液排泄。提出这些部分降解产物如何从溶酶体和细胞中逸出的机制。
3. 为缺乏α-N-乙酰半乳糖苷酶的患者尿液中含有O-聚糖的糖肽积累提供可能的解释。
4. 多泡体是如何产生的，它们有什么作用？
5. 在溶酶体贮积症中，使用酶抑制剂作为分子伴侣来恢复酶活性似乎违反直觉。解释这种治疗方法背后的原理。

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第45章 先天性糖基化障碍

1. 您如何定义“糖基化”障碍？描述当今用于识别糖基化障碍的方法。
2. 血清转铁蛋白有两个N-糖基化位点，每个聚糖由唾液酸的双天线糖链组成。您会预测先天性糖基化障碍（CDG）患者的哪种聚糖模式？
3. 哪些类型的细胞可能特别容易受到杂合性丧失或导致糖基化障碍的自发突变的影响？
4. 解释“功能获得”突变如何导致糖基化障碍。
5. 您将如何评估遗传和环境对糖基化障碍的贡献？

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第46章 获得性人类疾病中的聚糖

1. 选择素在各种疾病中的作用的共同潜在机制是什么？
2. 虽然肝素主要用作抗凝剂，但其使用已被提议与其他几种疾病有关。一种药物怎么可能与这么多不同的机制相关？
3. 举两个例子，其中糖基化的改变导致涉及造血干细胞的获得性血细胞疾病。为什么体细胞突变有可能产生表型？
4. 描述导致血细胞疾病、IgA 肾病和癌症糖基化改变中 O-糖发生变化的常见潜在分子机制。
5. 描述病原体如何利用宿主聚糖建立胃肠道和尿路感染。

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第47章 癌症的糖基化变化

1. 解释为什么单克隆抗体检测到的许多癌症特异性标志物被证明是针对聚糖表位的。
2. 许多癌细胞类型表现出N-糖的支链改变，粘蛋白的过度表达，透明质酸产生和周转的变化，以及硫酸乙酰肝素的表达和硫酸化降低。讨论这些变化是如何发生的，以及它们如何影响癌症的生长和转移。
3. 唾液酸-Tn表达是许多癌的突出特征。尽管负责其合成的酶并不总是上调，但如何解释这种表达的高频率？
4. 考虑选择素和选择素配体在癌症进展和转移中的潜在作用。
5. 聚糖结构的改变可用于诊断或治疗癌症的潜在方法有哪些？

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第48章 聚糖识别探针作为工具

1. 与植物凝集素相比，使用单克隆抗体来确定制剂中是否存在聚糖的优缺点是什么？
2. 使用凝集素或抗聚糖抗体确定组织、细胞或聚糖混合物中是否存在聚糖时，有哪些重要对照？
3. 从大量可用的凝集素中选择一个子集，以确定制备中寡甘露糖基、杂交型和复杂型N-糖的相对量。
4. 提出使用聚糖决定簇的单克隆抗体分离寡糖表达不足的突变细胞系的方法。
5. 通过观察基因同源性，您怀疑昆虫会产生一种新的β-葡糖醛酸酶，该酶作用于昆虫聚糖中存在的末端葡萄糖醛酸残基。提出一种非放射性方法来测量细胞提取物中这种酶的活性。

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第49章 培养的哺乳动物细胞的糖基化突变体

1. 与从突变动物或患有糖基化障碍的人类中提取细胞系相比，在培养细胞系中分离突变体的优缺点是什么？
2. 讨论用于分离突变体的不同方案的优缺点（即，使用凝集素或毒素进行选择，使用基因编辑策略，通过补体介导的裂解进行选择，通过复制板筛选以及通过流式细胞术进行分选）。
3. 在存在和不存在半乳糖和N-乙酰半乳糖胺的情况下，如何使用LDLD细胞来测试聚糖在生物过程中的作用？
4. 描述各种类型的功能获得性糖基化突变。考虑产生蛋白质糖基化位点的突变以及改变糖基化基因表达的突变。
5. 提出一种鉴定O-甘露糖聚糖合成中阻断的动物细胞突变体的方法。

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第50章 聚糖的结构分析

1. 描述去除N-糖的选择性方法和从糖蛋白中去除O-糖的选择性方法。
2. 低聚糖的分子量为972，但其NMR谱图是α-葡萄糖的单个单糖的分子量。甲基化分析得到单一产物，在 C-2、C-3 和 C-6 位置甲基化。聚糖结构是什么？
3. 核磁共振波谱中的哪些特征允许区分联动中的异常构型？
4. 描述一种非放射性标记程序，该程序允许在HPLC和TLC应用中灵敏地检测聚糖。
5. 命名质谱仪中使用的两种电离方法和两种质量分离方法。

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第51章 糖组学和糖蛋白组学

1. 生物体的“糖组”是什么？该生物体中的单个细胞是否不同？
2. 来自基因组和蛋白质组的哪些信息可能有助于预测细胞的糖组？
3. 糖组学和糖蛋白组学有什么区别？
4. 提出一种实验策略来表征组成糖组的不同聚糖亚型的序列和链接。例如，如何表征蛋白质相关的N-和O-聚糖的结构？
5. 质谱如何帮助表征蛋白质上的糖基化位点？

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第52章 糖生物信息学

1. 获得完整的聚糖结构数据库有哪些局限性？
2. 为什么糖生物信息学资源需要MIRAGE（糖组学实验所需的最小信息）等标准计划？
3. 对于相同的单糖组成，是否可以具有不同的唯一标识符？
4. 基因组学和蛋白质组学数据库的哪些方面可以链接到糖组学数据库？
5. 糖组学实验数据分析需要哪些类型的软件工具？

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第53章 聚糖和糖偶联物的化学合成

1. β-葡萄糖苷很容易通过利用C-2的保护基团来合成，能够参与邻近的基团。没有这种保护基团，大多数化学葡萄糖基化反应中的首选产物是α-葡萄糖苷。解释这一发现。
2. 为什么β-甘露糖苷如此难以化学生成？
3. 在聚糖的固相合成中，糖苷键最常构建为糖基受体与固体载体和溶液中活化的糖基供体结合。为什么这种情况比糖基供体与固体支持物结合的替代方法更受欢迎？
4. 苄基通常用作保护基团，以掩盖在最终低聚糖/糖缀合物合成中未修饰的醇官能团。解释原因。
5. 使用固相聚糖合成，可以合成重复的低聚糖，其大小可以超过溶液中可以达到的尺寸。解释原因，同时考虑到固相肽合成与溶液相肽合成相比提供的内在优势。

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第54章 聚糖和糖偶联物的化学酶促合成

1. 我们认为糖苷酶是切割而不是合成糖苷键的酶。如何操纵糖苷酶的底物和反应条件将其从降解酶转化为合成酶？
2. 酶促合成聚糖比化学合成相同结构的效率高得多，但大量聚糖的生产需要大量所需的糖基转移酶或糖苷酶。选择酶的来源，并解释为什么您认为在大量生产特定聚糖产品方面更有希望。
3. 在转糖基化事件中，平衡需要从水解转变为糖苷键形成。解释如何做到这一点，同时考虑到反应条件（底物、溶剂）。
4. 转糖基化也发生在自然界中。两类糖苷酶（转化糖苷酶或保留糖苷酶）中的哪一类更容易产生转糖基化？
5. 溶液相聚糖合成可以与酶促合成合并，以获得复杂的聚糖结构。将固相聚糖合成与酶促聚糖合成相结合有什么要求？

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第55章 抑制糖基化的化学工具

1. 解释谷氨酰胺抑制剂：果糖氨基转移酶（GFAT）如何影响糖基化？
2. 从机制的角度来看，抑制糖苷酶的生物碱怎么可能也阻断糖基转移酶呢？
3. 您将如何获得通过在Notch中的EGF重复序列中添加O-岩藻糖而引发的聚糖抑制剂？
4. 提出对半乳糖的化学修饰以产生唾液酸转移酶的抑制剂。
5. 酶抑制剂如何也能充当化学伴侣？

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第56章 糖基化工程

1. 为什么中国仓鼠卵巢（CHO）细胞是工业界用于生产人用重组糖蛋白药物的首选细胞系？
2. 列出工程细胞糖基化所需的重要设计元素。
3. 描述细菌、酵母、昆虫和哺乳动物细胞中 N-糖基化之间的差异，这对糖基化工程很重要。
4. 描述酵母和植物细胞中糖基化工程的示例，以增强溶酶体酶替代的递送。
5. 描述目前临床使用的重组抗体的糖工程工程示例，该抗体会影响其功能。
6. 描述精确基因编辑技术的主要原理。

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第57章 生物技术和制药工业中的聚糖

1. 解释流感神经氨酸酶抑制剂的作用机制。
2. 设计一种基于聚糖的治疗方法，通过阻断天然聚糖与完整（或活）微生物上的GBP相互作用而起作用。
3. CHO细胞产生的一部分促红细胞生成素（EPO）未完全唾液酸化（即，某些糖型在其N-糖上暴露了半乳糖残基）。可以向细胞培养基中添加哪些糖以提高EPO唾液酸化的总体水平？
4. 解释增加重组糖蛋白的糖基化程度如何增加其在体内的半衰期。
5. 描述在非人源培养的动物细胞中产生重组治疗蛋白的潜在有害影响。

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第58章 纳米技术中的聚糖

1. 亲和力和亲和力有什么区别？为什么这与糖偶联物特别相关？设计一种基于聚糖的治疗方法，通过阻断天然聚糖与完整（或活）微生物上的GBP相互作用而起作用。
2. 绘制蛋白质与聚糖或糖偶联物之间可以设想的所有多价模式的示意图。使用这些表示来显示糖胶质、糖聚合物和糖苷颗粒可能与蛋白质具有的不同相互作用模式。
3. 对于这些糖偶联物类型中的每一种，请解释首字母缩略词（如果适用），然后按大小的典型顺序排列：糖量子点、糖AuNP、糖 MNPs、糖富勒烯、糖碳纳米管、糖树枝状聚合物。尺寸如何影响这些在体内或体外的应用？
4. 各举一个例子（包括关键接头结构或键合模式），说明糖技术中的平台如何用共价或非共价聚糖修饰。
5. 列举糖聚糖技术在临床问题中的一些潜在应用。

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第59章 聚糖在生物能源和材料科学中的应用

1. 人类对植物聚糖的主要用途是什么？
2. 讨论将玉米粒中存在的淀粉发酵成生物乙醇的积极和消极影响。
3. 将生物质分解成糖可能需要哪些酶？
4. 纤维素的哪些化学改性会导致具有增强或新特性的多糖衍生物？
5. 描述纤维素纳米材料的一些用途。

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第60章 糖科学的未来方向

1. 向非专家解释为什么对糖科学的理解对于理解和治疗几乎所有影响人类的疾病至关重要。
2. 概括先天性糖基化疾病（CDG）告诉我们聚糖在人类发育和生物学中的作用。
3. 描述大规模聚糖阵列在传染病诊断和其他疾病研究中可能的未来价值。
4. 描述基因组学和蛋白质组学的进步如何加速糖生物学的进步。
5. 在本章的末尾，列出了糖生物学未来的一些主要基本问题。你能想到至少一个未列出的其他问题吗？

CHAPTER 1: HISTORICAL BACKGROUND AND OVERVIEW

1. What factors have deterred the integration of studies of the biology of glycans (“glycobiology”) into conventional molecular and cellular biology?

2. Why has evolution repeatedly selected for glycans to be the dominant molecules on all cell surfaces?

3. Explain how extracellular and nuclear/cytosolic glycans differ from one another.

4. What are the various factors that can affect glycan composition and structure on cell-surface and secreted molecules?

5. Discuss the various ways in which glycans participate in critical intracellular functions.

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CHAPTER 2: MONOSACCHARIDE DIVERSITY

1. What are the nine most common monosaccharides found in vertebrate glycans?

2. Define the following terms: D- and L-stereochemistry, epimer and anomer, axial and equatorial, reducing end and nonreducing end, and α- and β-linkages.

3. α-Glycosides of glucose position the aglycone group in the axial orientation, whereas α-glycosides of sialic acid position this group in the equatorial orientation. Explain this apparent discrepancy by applying the definitions of α- and β-anomeric stereochemistry to these two monosaccharides.

4. In nature, D-galactose can be converted to L-galactose in just two enzymatic steps. Using Fischer projections, show the chemical transformations that can accomplish this two-step interconversion.

5. Based on the atoms and functional groups within monosaccharides, describe the ways in which they might interact with proteins (e.g., electrostatic interactions, hydrogen bonding, van der Waals forces, and hydrophobic interactions).

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CHAPTER 3: OLIGOSACCHARIDES AND POLYSACCHARIDES

1. If there are 21 amino acids and only 10 major monosaccharides in eukaryotes, why are there so many more possible combinations of monosaccharides in a hexasaccharide than amino acids in a hexapeptide?

2. What amino acid serves as the aglycone of an N-linked oligosaccharide?

3. What is the repeating unit of chondroitin sulfate?

4. What unique structural characteristic contributes to the flexibility of heparan sulfate but not chondroitin sulfate?

5. Name three types of bacterial polysaccharides that serve as antigens.

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CHAPTER 4: CELLULAR ORGANIZATION OF GLYCOSYLATION

1. Consider the advantages and disadvantages of topologically restraining glycosylation to the ER/Golgi compartments.

2. What are the differences between physical and functional localization of glycan-modifying enzymes?

3. Describe mechanisms that determine Golgi localization of transferases.

4. Explain how localization of transferases can affect glycan composition of cell-surface and secreted molecules.

5. Propose functions for secreted soluble glycosyltransferases or sulfotransferases generated from membrane-bound enzymes.

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CHAPTER 5: GLYCOSYLATION PRECURSORS

1. “Essential” monosaccharides are defined as those that an organism cannot make de novo. Are there essential monosaccharides in mammals?

2. Why do animals usually not require mannose, fucose, or galactose in the diet? In what situations would an individual require dietary supplementation of any of these sugars?

3. Why are nucleotide sugar transporters required in ER and Golgi membranes? What might be the outcome of congenital mutations of nucleotide sugar transporters?

4. Why would humans fail to metabolize cellulose as a source of energy? How do cows and other ruminants metabolize cellulose?

5. Multiglycosyltransferase complexes may exist in the Golgi apparatus. How might such multienzyme complexes affect glycan synthesis?

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CHAPTER 6: GLYCOSYLTRANSFERASES AND GLYCAN-PROCESSING ENZYMES

1. Explain how glycosyltransferases achieve a strict donor substrate specificity.

2. Glycosyltransferases and glycosidases have been assigned to families in the CAZy database. What is the basis for assignment to a particular family?

3. Give an example of a glycosyltransferase that recognizes acceptor substrates possessing a specific peptide sequence motif or protein domain. Explain why this glycosyltransferase may have evolved to possess such acceptor specificity.

4. What is meant by the terms “inverting” and “retaining” when used to describe a glycosidase or glycosyltransferase? In mechanistic terms, what do we know about how inverting glycosyltransferases catalyze their reactions?

5. Why is the Km of a glycosyltransferase, for both its donor and acceptor substrates, an important parameter in establishing what glycan structures are produced by a cell?

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CHAPTER 7: BIOLOGICAL FUNCTIONS OF GLYCANS

1. What are the different ways in which glycans can mediate or modulate biological functions?

2. Explain the difference between intrinsic and extrinsic functions of glycans.

3. Why are the biological consequences of altering glycosylation in cultured cells and intact animals so variable?

4. Given intra- and interspecies variations in glycosylation, how can one narrow down critical functions?

5. Why does it appear that some glycans may not have specific functions when their assembly is genetically determined?

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CHAPTER 8: A GENOMIC VIEW OF GLYCOBIOLOGY

1. What is a sequence-based classification of glycosyltransferases?

2. Describe the ways in which gene sequences predict or fail to predict functionality in transferases, hydrolases, and glycan-binding proteins.

3. Give examples of bifunctional enzymes involved in glycosylation. Suggest the driving force for the evolution of bifunctional transferases.

4. What can you learn about the way of life of an organism (“ecology”) based on the relative number of glycosidase and glycosyltransferase genes in its genome?

5. How could an organism effectively augment the number of glycosidases and glycosyltransferases at its disposal?

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CHAPTER 9: N-GLYCANS

1. What are some advantages for a glycoprotein in having a large number of N-glycosylation sites?

2. Consider the topology of N-glycosylation and provide possible explanations for segregating the formation of Man5GlcNAc2-Dol from the formation of Glc3Man9GlcNAc2-Dol.

3. How is N-glycan biosynthesis different in yeast, invertebrates, plants, and mammals?

4. What is N-glycan microheterogeneity? What might be some advantages of N-glycan microheterogeneity?

5. Describe how the branching of N-glycans can regulate growth factor signaling.

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CHAPTER 10: O-GalNAc GLYCANS

1. What are the factors that determine the O-GalNAc glycan composition of a cell?

2. What characteristics make a polypeptide a good acceptor for O-GalNAc glycosylation? Can you predict sites of O-GalNAc glycosylation based on these characteristics?

3. How does the assembly of O-GalNAc glycans differ from the assembly of N-glycans?

4. Explain the most important functional features of a typical secreted mucin.

5. What are the advantages of having so many polypeptide-N-acetylgalactosaminyltransferases?

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CHAPTER 11: GLYCOSPHINGOLIPIDS

1. The lipid moiety of glycosphingolipids, ceramide, endows them with self-associating properties in the plane of the membrane. Explain why.

2. Glycosphingolipids function via cis regulation and trans recognition. Explain these terms and provide examples of each.

3. Some humans and experimental animals with mutations in the enzyme responsible for glucosylceramide breakdown suffer from dehydration. Explain why.

4. Several human lysosomal storage diseases result from mutations in the enzymes responsible for breakdown of glycosphingolipids leading to toxic buildup of the uncleaved substrate. Similar buildup of glycosphingolipids sometimes occurs even when there is ample enzyme present. Explain why.

5. The animal brain is enriched in glycosphingolipids compared to other glycan classes. Describe two distinct structural classes of brain glycosphingolipids and two examples of their physiological functions.

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CHAPTER 12: GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORS

1. What do GSLs and GPI anchors have in common? How do they differ?

2. Describe differences in the behavior of proteins that have transmembrane domains from those with GPI anchors.

3. Explain how GPI-anchored proteins might facilitate signal transduction across the plasma membrane.

4. Devise an assay to measure the distribution of GPI anchor intermediates across the ER membrane and the mechanism for flipping intermediates across the ER.

5. Why are clinical symptoms of diseases caused by glycosylphosphatidylinositol biosynthetic defects so variable?

6. How is the GPI biosynthetic pathway in Trypanosoma brucei or yeast different from that in humans? What implications does elucidation of these differences have for our understanding and manipulation of the GPI pathway?

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CHAPTER 13: OTHER CLASSES OF EUKARYOTIC GLYCANS

1. Propose a mechanism that could explain how altering the glycosylation of Notch affects the binding of different Notch ligands.

2. Why do you think a protein like ADAMTS13, which has eight tandem TSRs, requires POFUT2 for proper folding?

3. What advantage is there in the O-mannose matriglycan on α-dystroglycan compared to simpler O-mannose glycans?

4. What effects could O-glycosylation of collagens have on their folding and/or structure?

5. C-mannosylated tryptophan was first detected in human urine. Provide an explanation for why this amino acid glycoside was excreted into the urine rather than as free tryptophan and mannose.

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CHAPTER 14: STRUCTURES COMMON TO DIFFERENT GLYCANS

1. Propose a function for the allelic variation observed in the ABO blood group system. Nonprimates do not express the ABO locus—how does this affect your answer?

2. Hyperacute (graft) rejection (HAR) occurs after transplantation of organs from nonhuman donors into humans and results from an immediate reaction of circulating anti-Galα1-3Gal antibodies with the transplanted tissue. Suggest ways to modify the donor or recipient to prevent HAR.

3. Compare and contrast “LacNAc” and “LacdiNAc” units. How does the presence of these terminal disaccharides affect the addition of sialic acid and fucose?

4. Based on what you know about terminal structures on follicle-stimulating hormone and lutropin, propose several glycan-based mechanisms that could account for infertility in humans.

5. Certain strains of Escherichia coli bind to P blood group antigens and cause urinary tract infections. What evolutionary advantage might exist for retaining the transferases that make a deleterious glycan?

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CHAPTER 15: SIALIC ACIDS AND OTHER NONULOSONIC ACIDS

1. Compare and contrast the structure of sialic acids with other monosaccharides.

2. What advantages does sialic acid diversity provide in vertebrate systems?

3. What are the unique features of the sialic acid biosynthetic pathways in comparison to those of other monosaccharides?

4. How would you determine if a previously unstudied organism contains sialic acids?

5. Contrast the addition of α2-6-linked sialic acids to O-GalNAc glycans and N-glycans and their recognition by sialic acid–binding lectins.

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CHAPTER 16: HYALURONAN

1. Why do small molecules diffuse readily through a high-molecular-weight hyaluronan (HA) solution such as the vitreous of the eye, whereas larger macromolecules (e.g., certain proteins) do not?

2. What are some of the dominant physical and molecular factors that influence diffusion rate through HA solution, and how might the rate be different in a purely HA matrix or in a heterogeneous extracellular matrix consisting only partially of HA?

3. HA solutions have unusual viscoelastic properties; for example, HA acts like a gel, yet it can function as a lubricant. How do you explain these properties in terms of the molecular structure of the chains?

4. Why are HA-binding proteins considered lectins, but proteins that bind to sulfated glycosaminoglycans are not? How do these two classes of glycan-binding proteins differ?

5. How could a cell-surface HA receptor (e.g., CD44) respond differently to HA oligosaccharides with 6–10 sugar units compared to high-molecular-weight HA? Why might different responses need to be elicited through the same receptor?

6. How would you demonstrate whether an HA chain assembles from the reducing end versus the nonreducing end?

7. How would you demonstrate hyaluronidase activity of a new putative hyaluronidase family member in vivo or in a cellular context? Specifically, how could you distinguish HA degradation from HA clearance if it occurred intracellularly?

8. High-molecular-weight HA has been shown to have tissue-protective effects in lung pathologies, but the presence of high-molecular-weight HA is also obstructive to lung function. How can these observations be reconciled? Is there a way to overcome these contrasting impacts of HA so it can be used effectively as a therapeutic?

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CHAPTER 17: PROTEOGLYCANS AND SULFATED GLYCOSAMINOGLYCANS

1. What factors can affect the fine structure of sulfated glycosaminoglycans in cells?

2. Overexpression of Ext2 (which is part of the heparan sulfate copolymerase complex) increases the extent of sulfation of the chain. Provide an explanation for this finding.

3. Compare and contrast the biological functions of GPI-anchored proteoglycans from those that contain transmembrane domains.

4. Give examples of ways to modify the metabolism of glycosaminoglycans in cells and animals.

5. What are the options for generating drugs based on glycosaminoglycan–protein interactions?

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CHAPTER 18: NUCLEOCYTOPLASMIC GLYCOSYLATION

1. What biochemical criteria would you require to demonstrate the attachment of a glycan to a specific nuclear or cytoplasmic protein?

2. What conventional glycosylation pathways have steps that occur on the cytoplasmic side of membranes that could be a source of nucleocytoplasmic glycans?

3. Compare and contrast the initiating glycosylation reactions on mucins, proteoglycans, Notch, glycogenin, and Skp1.

4. How would you demonstrate the presence of glycosaminoglycans in the nucleus?

5. Give examples of glycoconjugates that are initially formed in the cytoplasm but later transit to and function at the cell surface or in the extracellular space.

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CHAPTER 19: THE O-GlcNAc MODIFICATION

1. O-GlcNAc is now known to be the most common form of glycosylation in the cell. Why did it take so long for this fact to be appreciated? What was the serendipity involved in its discovery?

2. O-GlcNAc is thought to compete with phosphorylation for the same or similar sites on nuclear or cytoplasmic glycoproteins. What are the similarities and differences between O-GlcNAcylation and phosphorylation?

3. What are the mechanistic differences between O-GlcNAc glycosylation and cell-surface glycosylation?

4. How does O-GlcNAc act as a “metabolic sensor”?

5. Speculate as to how O-GlcNAc might contribute to “glucose toxicity” in diabetes.

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CHAPTER 20: EVOLUTION OF GLYCAN DIVERSITY

1. What processes could maintain glycan gene polymorphisms (i.e., structural heterogeneity) within populations?

2. What changes in sialic acid biology occurred during human evolution?

3. Is it possible to predict glycan function by examining glycan composition across phylogeny?

4. What are the problems in using “comparative glycobiology” for determining evolutionary relationships (phylogeny)?

5. Which glycosylation pathways support a common origin of eukaryotes?

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CHAPTER 21: EUBACTERIA

1. Plants, bacteria, and yeast all have cell walls that provide resistance to osmotic pressure. Compare the composition and architecture of these barriers.

2. Both bacteria and animal cells utilize polyisoprenoids for the assembly of glycans. Compare and contrast these lipid intermediates.

3. Compare the structure of lipopolysaccharide to glycerolipids and gangliosides.

4. Cell wall biosynthesis in Gram-negative bacteria requires a coordinated synthesis of peptidoglycan and LPS. Propose potential regulatory mechanisms that ensure homeostasis.

5. Compare the architecture of the mycobacterial and Gram-negative cell wall.

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CHAPTER 22: ARCHAEA

1. Compare and contrast the pathways of glycoprotein N-glycosylation in Archaea, Bacteria, and eukaryotes.

2. All cells produce acidic glycans, but the source of the negative charge varies. What are the acidic groups on the glycans present in Escherichia coli, Archaea, yeast, and animal cells?

3. Compare the S-layer in Archaea with surface glycoproteins in eukaryotic cells.

4. Search for molecular similarities in the extracellular matrix of eukaryotes and the archaeal cell wall.

5. Compare the bacterial murein and the archaeal pseudomurein.

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CHAPTER 23: FUNGI

1. Compare the composition and structure of yeast cell walls and the envelope of Gram-negative bacteria.

2. What changes in the yeast cell wall might occur in a mutant that produces less β-glucan? What effects might an abnormal cell wall have on the shape, growth, or viability of this mutant?

3. Compare and contrast N-glycan synthesis in yeast and mammals. What is the functional significance of the differences?

4. Describe a unique feature of GPI-linked proteins in fungi. How does this process change protein localization in these organisms?

5. A pharmaceutical company has hired you to assess glycan synthesis as a target for drug development to combat a newly described and highly virulent pathogenic fungus. Describe a set of reasonable targets and some important issues you need to consider.

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CHAPTER 24: VIRIDIPLANTAE AND ALGAE

1. Why do plants that do not express sugars present in animal cells (e.g., sialic acids) have lectins that bind to glycans containing these sugars?

2. Pectins in plants are sometimes compared to glycosaminoglycans in animals. How do they differ? How are they similar?

3. Why are recombinant mammalian glycoproteins generated in plants immunogenic?

4. Compare the structures of glycoglycerolipids in plants, lipid A in bacteria, and glycosphingolipids in animals.

5. Elicitors and Nod factors are active at very low concentration, and therefore one might predict that their affinity for their signal-transducing receptors would be very high (in the pM range). Based on what you know about other glycan-binding proteins, how would such high affinity be achieved?

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CHAPTER 25: NEMATODA

1. Propose some evolutionary forces driving the large expansion of some glycosyltransferase families in Caenorhabditis elegans (e.g., fucosyltransferases) compared with others (e.g., mannosyltransferases).

2. Compare and contrast chondroitin proteoglycan synthesis in C. elegans and in vertebrates.

3. How would you go about selecting mutants of C. elegans defective in N-glycan formation?

4. In contrast to vertebrate systems, O-GlcNAc addition to nuclear and cytoplasmic proteins is dispensable in C. elegans. How do you explain this finding?

5. Given the absence of sialic acids in C. elegans, what might you predict about the types and specificity of glycan-binding proteins in C. elegans?

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CHAPTER 26: ARTHROPODA

1. Compare and contrast what happens to the first N-acetylglucosamine residue attached to the mannosyl core of an N-glycan in Drosophila, Caenorhabditis elegans, and vertebrates.

2. Compare the structural differences in the O-glycan modifications of Drosophila Notch with those of vertebrate Notch EGF repeats. Why is Notch glycosylation in Drosophila less complex than in vertebrates?

3. Compare the core structure of glycosphingolipids in Drosophila with those present in C. elegans and vertebrates. How do the outer chains differ?

4. Transgenic expression of a β1-4 galactosyltransferase substitutes for Egghead (egh), which is a mannosyltransferase. What does this tell you about the function of the glycans present in Drosophila glycosphingolipids?

5. Explain how the overexpression or deletion of dally, a glypican homolog, can reduce the diffusion of a morphogen, such as dpp.

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CHAPTER 27: DEUTEROSTOMES

1. In studying the glycoproteins that mediate sperm–egg interactions during fertilization, why is it important to use several model animals?

2. If you were an enzymologist, how would you study the synthesis of fucose sulfate polymers?

3. Sulfated fucans are also extremely potent inhibitors of coagulation and inflammation in mammalian systems. Propose a mechanism for this action based on the similarity of their structure to other bioactive glycans.

4. Why do some glycan-related gene knockouts in laboratory mice exhibit no obvious phenotype?

5. If you were to discover a new glycan in humans, which model organism(s) would you pick for further studies and how would you manipulate it genetically?

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CHAPTER 28: DISCOVERY AND CLASSIFICATION OF GLYCAN-BINDING PROTEINS

1. How are sulfated glycosaminoglycan-binding proteins distinguished from lectins?

2. Suppose you discovered a new glycan-binding protein. How would you determine its classification?

3. Compare and contrast the functions of soluble and membrane-bound lectins.

4. Contrast the functions of animal lectins that recognize self and non-self glycans.

5. Compare the methods for characterizing glycan-binding proteins in organisms with well-annotated whole genomes with those from organisms in which whole-genome sequences are unavailable.

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CHAPTER 29: PRINCIPLES OF GLYCAN RECOGNITION

1. What determines the affinity of a glycan for a GBP?

2. Many types of protein–glycan interactions are low affinity, and in some cases high avidity is achieved by clustering receptors and ligands. What are the advantages and disadvantages of achieving high-affinity interactions through multivalency?

3. How does the density of glycan ligands affect binding of a GBP? Is this relevant in vivo?

4. Provide examples of GBPs that bind with relatively low affinity to highly abundant glycans and other GBPs that bind with relatively high affinity to glycans that are scarce.

5. To measure the binding kinetics and/or affinity of a GBP to a glycan, there are several techniques, including isothermal titration calorimetry and surface plasmon resonance. Choose one of these or other techniques and design an experiment to measure the Ka of binding, assuming the glycan is easy to derivatize, if needed, at its reducing end.

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CHAPTER 30: STRUCTURAL BIOLOGY OF GLYCAN RECOGNITION

1. Cholera toxin binds to the ganglioside GM1 with high affinity (Kd ∼ 0.1 nm) relative to the binding of many other GBPs to their ligands (which exhibit Kd values in the range of 0.1 µm to 0.1 mm). How do you explain this observation?

2. Name four types of molecular interactions important in carbohydrate recognition.

3. What amino acid residues are likely to play important roles in binding highly sulfated glycosaminoglycans?

4. What NMR experiment can return information on glycan geometry as it exists in the protein-bound state?

5. Name a database in which you can find structures of GBPs.

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CHAPTER 31: R-TYPE LECTINS

1. Describe the differences and similarities between Ricinus communis agglutinin-I and ricin.

2. For ricin and other ribosome-inactivating toxins to kill cells, they must first gain access to the cytoplasm. How does this occur? How would you exploit this mechanism to deliver cargo to different sites in a cell?

3. Explain how a cell that becomes resistant to one type of toxic lectin could become sensitive to another.

4. What are the functions of R-type lectin domains found in enzymes such as glycosyltransferases and glycosidases?

5. Describe examples of animal lectins in cells that engage glycan ligands in both cis and trans topologies.

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CHAPTER 32: L-TYPE LECTINS

1. Describe possible functions for L-type plant lectins present in the seeds of leguminous plants.

2. If L-type lectins are involved in defense, why does each plant produce only a very limited number of lectins?

3. Why are both plant seed lectins and GBPs involved in protein quality control classified as L-type lectins?

4. Compare and contrast the “jelly-roll” fold in L-type lectins, the C-type lectin fold, and the link module.

5. Plant lectins are typically glycoproteins and therefore mature through the ER/Golgi secretory pathway. Propose a mechanism to prevent their interaction with other Golgi glycoproteins during their assembly and secretion.

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CHAPTER 33: P-TYPE LECTINS

1. Why was it important to use a double-labeled substrate donor [β-32P]UDP[3H]GlcNAc in studies of Man-6-P recognition marker biosynthesis?

2. Compare and contrast the process of assembling the Man-6-P recognition marker on lysosomal enzymes via formation of GlcNAc-P-Man and subsequent removal of the N-acetylglucosamine moiety versus a mannose-specific ATP-dependent kinase.

3. The Man-6-P recognition marker assembles mainly on lysosomal enzymes by selective recognition of peptide determinants in the substrate proteins by GlcNAc-P-transferase. Describe other examples of selective modification of glycans on subsets of glycoproteins. How do the recognition determinants differ?

4. How would the number of N-glycans on a lysosomal enzyme affect its affinity for one of the Man-6-P receptors?

5. Compare and contrast the packaging of the Man-6-P receptors into clathrin-coated vesicular carriers at the trans-Golgi network versus the cell surface.

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CHAPTER 34: C-TYPE LECTINS

1. Many proteins that contain C-type lectin domains do not bind glycans, and the ones that do are called C-type lectins. What is the difference in structure that distinguishes these two classes of proteins?

2. Why is it difficult to predict the type of glycan to which a C-type lectin will bind?

3. Some C-type lectins can form oligomers, which greatly increase the avidity of interactions with glycan ligands. Explain how oligomerization can also affect the specificity of the interaction.

4. Some C-type lectins, notably the selectins, bind with higher affinity to some glycoproteins than to others on the same cell, even though several glycoproteins may display similar glycan structures. Consider mechanisms that confer such preferential binding.

5. Compare the interaction of P-selectin with PSGL-1 to the binding of a plant lectin to PSGL-1.

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CHAPTER 35: I-TYPE LECTINS

1. There are now more than a dozen human Siglecs known. Why were these and other sialic acid–binding proteins not discovered until relatively recently?

2. Compare the potential function of Siglecs with inhibitory motifs in their cytosolic tails with those that can recruit activating motifs.

3. Why are Siglec homologs found primarily in “higher” animals?

4. Explain the likely mechanisms and driving forces for the rapid evolution of some Siglecs.

5. Why do plants and invertebrates that do not express sialic acids have sialic acid–binding proteins?

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CHAPTER 36: GALECTINS

1. How do you explain the finding that galectins are not routinely found in large amounts in body fluids, even though most of them are soluble proteins and are often found extracellularly?

2. Why do changes in glycan branching pathways and sialylation have the potential to impact galectin function?

3. How do galectins achieve high-affinity binding to cell-surface glycans? How do galectins form lattices with cell-surface glycans?

4. Explain how a galectin, as an innate immune effector, might act as a receptor to fight microbial infection.

5. Galectins bind to a variety of cells and trigger various responses in different cell types. How do galectins send signals through cell-surface receptors?

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CHAPTER 37: MICROBIAL LECTINS: HEMAGGLUTININS, ADHESINS, AND TOXINS

1. What kinds of cytoplasmic glycosylation events are associated with infection and pathology?

2. Compare the carbohydrate-recognition domains of bacterial and viral adhesins to those of animals and plant lectins.

3. What agents other than simple sugars could be used for anti-adhesion therapy of microbial diseases?

4. A serious problem limiting the use of antibiotics is the rapid emergence of resistant bacteria. To what extent could this also become a problem with anti-adhesion therapy?

5. Multivalent and polyvalent sugars are more powerful inhibitors of microbial lectins than simple monomeric ones. Explain the reasons for this phenomenon and discuss its applications.

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CHAPTER 38: PROTEINS THAT BIND SULFATED GLYCOSAMINOGLYCANS

1. Proteins that bind to sulfated glycosaminoglycans (GAGs) are not considered lectins. Why?

2. The extent of modification of heparin is much greater than that of heparan sulfate. How would this affect conformation and the interaction of GAG-binding proteins?

3. What are the main types of bonding forces that contribute to GAG-protein interactions?

4. Interactions between proteins and sulfated glycosaminoglycans are important in various physiological and pathophysiological settings. Are they specific?

5. Explain how HS plays similar roles in promoting antithrombin–thrombin interactions and FGF–FGFR interactions?

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CHAPTER 39: GLYCANS IN GLYCOPROTEIN QUALITY CONTROL

1. What are the prerequisites for protein-bound glycans to function as signaling molecules in protein folding and quality control?

2. Describe the types of chaperones present in the ER.

3. The addition and removal of glucose residues constitutes part of the quality control system for monitoring protein folding. What is the role of mannose trimming?

4. How is the ER stress response (ERAD) coordinated with N-glycan synthesis?

5. Compare the processing of N-glycans in the ER and Golgi with degradative pathways for N-glycans in lysosomes and in the cytoplasm.

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CHAPTER 40: FREE GLYCANS AS BIOACTIVE MOLECULES

1. What are the advantages of using glycans derived from host organisms as signals of danger?

2. How can glycans mediate the interaction between nonglycan signals and their receptors?

3. Can you think of disadvantages of the use of glycans as pathogen-associated molecular patterns (PAMPs) by host immune systems?

4. What structural modifications of generic chitin oligosaccharide Nod factors provide host specificity in the bacterial–plant interactions that lead to root nodule formation and nitrogen fixation in legumes?

5. How can you explain the observation that different β-glucans trigger plant immune systems through different PRRs?

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CHAPTER 41: GLYCANS IN SYSTEMIC PHYSIOLOGY

1. If glycans have roles in almost every aspect of systemic physiology, why can loss of a glycosyltransferase and subsequent alteration of glycan structure in some cases have no obvious effect on development or physiology?

2. Explain the evidence supporting the idea that glycans and GBPs are involved in immune responses.

3. How does differential glycosylation regulate the plasma half-life of glycoproteins, and where are these glycoproteins cleared?

4. What are the different functions of glycans on mucins on different epithelial surfaces?

5. How do glycans regulate neuronal growth and repair?

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CHAPTER 42: BACTERIAL AND VIRAL INFECTIONS

1. How can bacteria benefit by coating their surface with a polysaccharide capsule?

2. How do pathogenic bacteria initially colonize tissues?

3. Would a mouse lacking Toll-like receptor 4 be more or be less susceptible to bacterial infection? What about susceptibility to lipopolysaccharide-induced sepsis?

4. How do influenza and herpes simplex virus engage the host cell surface to initiate infection?

5. Can one manipulate glycans to prevent or treat microbial infection?

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CHAPTER 43: PARASITIC INFECTIONS

1. Explain the role of glycoconjugates in the high fever typically associated with the pathogenesis of malaria.

2. How do African trypanosomes avoid destruction by the immune system after inoculation by the bite of the tsetse fly?

3. What is the mechanism by which the protozoan parasite Leishmania attaches and eventually detaches from its sandfly vector midgut during transmission?

4. Many glycans made by the parasitic worm Schistosoma mansoni are highly antigenic in the infected hosts. What property of these glycans makes them so antigenic, and would this offer a possibility to make a vaccine?

5. What glycosyltransferases and sugar/nucleotide sugar transporters may be unique to parasites and therefore potential targets for chemotherapeutic intervention?

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CHAPTER 44: GENETIC DISORDERS OF GLYCAN DEGRADATION

1. Predict which glycans and tissues/organs would be affected most if β-galactosidase was altered.

2. In lysosomal storage disorders, undegraded or partially degraded glycans and glycopeptides are often excreted in the urine. Propose a mechanism for how these partial degradation products escape from lysosomes and cells.

3. Provide possible explanations for the accumulation of glycopeptides with O-glycans in the urine of patients deficient in α-N-acetylgalactosaminidase.

4. How do multivesicular bodies arise and what purpose do they serve?

5. It would seem counterintuitive to use an enzyme inhibitor as a molecular chaperone to restore enzyme activity in a lysosomal storage disorder. Explain the rationale behind this therapeutic approach.

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CHAPTER 45: CONGENITAL DISORDERS OF GLYCOSYLATION

1. How do you define a “glycosylation” disorder? Describe the methods used today to identify a glycosylation disorder.

2. Serum transferrin has two N-glycosylation sites, and each glycan consists of biantennary sugar chains with sialic acid. What kinds of glycan patterns would you predict in patients with congenital disorders of glycosylation (CDGs)?

3. What types of cells might be especially susceptible to loss of heterozygosity or spontaneous mutations that cause glycosylation disorders?

4. Explain how “gain-of-function” mutations can cause a glycosylation disorder.

5. How would you assess the genetic and environmental contributions to a glycosylation disorder?

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CHAPTER 46: GLYCANS IN ACQUIRED HUMAN DISEASES

1. What are the common underlying mechanisms for the roles of selectins in various diseases?

2. Although heparin is primarily used as an anticoagulant, its use has been proposed in connection with several other diseases. How can one drug have relevance to so many different mechanisms?

3. Give two examples in which altered glycosylation has resulted in acquired blood cell diseases involving the hematopoietic stem cell. Why is it possible for somatic mutations to give rise to a phenotype?

4. Describe the common underlying molecular mechanism that causes changes in O-glycans in blood cell diseases, in IgA nephropathy, and in the altered glycosylation of cancer.

5. Describe how pathogens exploit host glycans in establishing gastrointestinal and urinary tract infections.

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CHAPTER 47: GLYCOSYLATION CHANGES IN CANCER

1. Explain why many cancer-specific markers detected by monoclonal antibodies turn out to be directed against glycan epitopes.

2. Many cancer cell types exhibit altered branching of N-glycans, excessive expression of mucins, changes in hyaluronan production and turnover, and decreased expression and sulfation of heparan sulfate. Discuss how these changes come about and how they would affect cancer growth and metastasis.

3. Sialyl-Tn expression is a prominent feature of many carcinomas. What explains the high frequency of this expression despite the fact that the enzyme responsible for its synthesis is not always up-regulated?

4. Consider the potential roles of selectins and selectin ligands in cancer progression and metastasis.

5. What are the potential ways in which alterations in glycan structure could be used advantageously for diagnosing or treating cancer?

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CHAPTER 48: GLYCAN-RECOGNIZING PROBES AS TOOLS

1. What are the advantages and disadvantages of using monoclonal antibodies versus plant lectins for determining the presence or absence of glycans in a preparation?

2. What are important controls when using lectins or antiglycan antibodies to determine the presence or absence of a glycan in a tissue, on a cell, or in a mixture of glycans?

3. Select from the large number of available lectins a subset that would allow you to determine the relative amounts of oligomannosyl, hybrid, and complex type N-glycans in a preparation.

4. Propose methods for using a monoclonal antibody to a glycan determinant for the isolation of a mutant cell line deficient in the expression of the glycan.

5. By observing gene homology, you suspect that insects produce a novel β-glucuronidase that acts on terminal glucuronic acid residues present in insect glycans. Propose a nonradioactive method to measure the activity of this enzyme in cell extracts.

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CHAPTER 49: GLYCOSYLATION MUTANTS OF CULTURED MAMMALIAN CELLS

1. What are the advantages and disadvantages of isolating mutants in cultured cell lines compared to deriving cell lines from mutant animals or humans afflicted with glycosylation disorders?

2. Discuss the advantages and disadvantages of different schemes used to isolate mutants (i.e., selection with lectins or toxins, using gene editing strategies, selection by complement-mediated lysis, screening by replica plating, and sorting by flow cytometry).

3. How might you use ldlD cells, in the presence and absence of galactose and N-acetylgalactosamine, to test the role(s) of glycans in biological processes?

4. Describe various types of gain-of-function glycosylation mutations. Consider mutations that create protein glycosylation sites as well as those that change the expression of glycosylation genes.

5. Propose a method to identify animal cell mutants blocked in the synthesis of O-mannose glycans.

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CHAPTER 50: STRUCTURAL ANALYSIS OF GLYCANS

1. Describe a selective way of removing N-glycans and a selective way of removing O-glycans from a glycoprotein.

2. An oligosaccharide has a molecular weight of 972, and yet its NMR spectrum is that of a single monosaccharide of α-glucose. Methylation analysis yields a single product, methylated at the C-2, C-3, and C-6 positions. What is the glycan structure?

3. What characteristic in an NMR spectrum allows distinction of anomeric configuration in a linkage?

4. Describe a nonradioactive tagging procedure that allows sensitive detection of glycans in HPLC and TLC applications.

5. Name two types of ionization methods and two types of mass separation methods used in mass spectrometers.

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CHAPTER 51: GLYCOMICS AND GLYCOPROTEOMICS

1. What is the “glycome” of an organism? Does it differ for individual cells in that organism?

2. What information from the genome and the proteome might be useful in predicting a cell's glycome?

3. What is the difference between glycomics and glycoproteomics?

4. Propose an experimental strategy to characterize the sequence and linkages of different glycan subtypes that comprise the glycome. For example, how might protein-associated N- and O-glycans be structurally characterized?

5. How can mass spectrometry help to characterize the sites of glycosylation on a protein?

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CHAPTER 52: GLYCOBIOINFORMATICS

1. What are the limitations of obtaining a complete database of glycan structures?

2. Why are standards initiatives such as MIRAGE (Minimum Information Required for A Glycomics Experiment) required for glycobioinformatics resources?

3. Is it possible to have different unique identifiers for the same monosaccharide composition?

4. What aspects of genomics and proteomics databases could be linked to glycomics databases?

5. What types of software tools are required for glycomics experimental data analysis?

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CHAPTER 53: CHEMICAL SYNTHESIS OF GLYCANS AND GLYCOCONJUGATES

1. β-Glucosides are readily synthesized by exploiting protecting groups at C-2 capable of neighboring group participation. Without such protecting groups, the preferred product in most chemical glucosylation reactions is the α-glucoside. Explain this finding.

2. Why are β-mannosides so difficult to generate chemically?

3. In solid phase synthesis of glycans, glycosidic bonds are most often constructed with the glycosyl acceptor bound to the solid support and the activated glycosyl donor in solution. Why is this situation preferred to the alternative approach in which the glycosyl donor is bound to the solid support?

4. Benzyl groups are often used as protective groups to mask those alcohol functions that are unmodified in the final oligosaccharide/glycoconjugate synthesized. Explain why.

5. Using solid phase glycan synthesis, repeating oligosaccharides can be synthesized of a size exceeding the size that can be attained in solution. Explain why, also considering the intrinsic advantages solid phase peptide synthesis offers in comparison with solution phase peptide synthesis.

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CHAPTER 54: CHEMOENZYMATIC SYNTHESIS OF GLYCANS AND GLYCOCONJUGATES

1. We think of glycosidases as enzymes that cleave rather than synthesize glycosidic bonds. How are the substrates and reaction conditions of glycosidases manipulated to convert them from degrading enzymes to synthetic enzymes?

2. Enzymatic synthesis of glycans can be far more efficient than chemical synthesis of the same structures, but production of large quantities of a glycan requires significant amounts of the required glycosyltransferases or glycosidases. Pick a source of enzymes and explain why you think it is more promising with respect to production of specific glycan products in large quantity.

3. In a transglycosylation event, the equilibrium needs to be shifted from hydrolysis to glycosidic bond formation. Explain how this can be done, taking into consideration the reaction conditions (substrates, solvents).

4. Transglycosylation also happens in nature. Which of the two classes of glycosidases—inverting glycosidases or retaining glycosidases—would be more prone to give transglycosylation?

5. Solution phase glycan synthesis can be merged with enzymatic synthesis to arrive at complex glycan structures. What would be the requirements to combine solid phase glycan synthesis with enzymatic glycan synthesis?

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CHAPTER 55: CHEMICAL TOOLS FOR INHIBITING GLYCOSYLATION

1. Explain how an inhibitor of glutamine:fructose aminotransferase (GFAT) would affect glycosylation?

2. From a mechanistic point of view, how can an alkaloid that inhibits a glycosidase also block a glycosyltransferase?

3. How would you go about obtaining an inhibitor of glycans that are initiated by the addition of O-fucose to EGF repeats in Notch?

4. Propose chemical modifications to galactose to create an inhibitor of sialyltransferases.

5. How can an enzyme inhibitor also act as a chemical chaperone?

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CHAPTER 56: GLYCOSYLATION ENGINEERING

1. Why are Chinese hamster ovary (CHO) cells the preferred cell line used by industry to produce recombinant glycoprotein drugs for human use?

2. List important design elements required for engineering cellular glycosylation.

3. Describe differences between N-glycosylation in bacteria, yeast, insect, and mammalian cells that are important for glycosylation engineering.

4. Describe examples of glycosylation engineering in yeast and plant cells for enhanced delivery of lysosomal enzyme replacement.

5. Describe an example of glycoengineering of a recombinant antibody currently in clinical use that affects its function.

6. Describe the main principles of precise genetic editing technologies.

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CHAPTER 57: GLYCANS IN BIOTECHNOLOGY AND THE PHARMACEUTICAL INDUSTRY

1. Explain the mechanism of action of influenza neuraminidase inhibitors.

2. Design a glycan-based therapeutic that acts by blocking the interaction of a naturally occurring glycan with GBPs on an intact (or live) microbe.

3. A portion of erythropoietin (EPO) produced by CHO cells is not fully sialylated (i.e., some glycoforms have exposed galactose residues on their N-glycans). What sugars might be added to the cell culture media to increase the overall level of EPO sialylation?

4. Explain how increasing the extent of glycosylation of recombinant glycoproteins can increase their half-life in vivo.

5. Describe the potential deleterious effects of producing recombinant therapeutic proteins in cultured animal cells of nonhuman origin.

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CHAPTER 58: GLYCANS IN NANOTECHNOLOGY

1. What is the difference between avidity and affinity? Why is this particularly relevant to glycoconjugates? Design a glycan-based therapeutic that acts by blocking the interaction of a naturally occurring glycan with GBPs on an intact (or live) microbe.

2. Draw schematic representations for all the modes of multivalency that you can envisage between a protein and a glycan or glycoconjugate. Use these representations to show the different modes of interaction that glycodendrimers, glycopolymers, and glyconanoparticles might have with a protein.

3. For each of these glycoconjugate types explain the acronym (where applicable) and then place in typical order of size: glycoQDs, glycoAuNPs, glycoMNPs, glyco-fullerenes, glycoCNTs, glyco-dendrimers. How might size affect the application of any of these in vivo or in vitro?

4. Give one example each (including key linker structures or bonding patterns) of how platforms in glyconanotechnology can be decorated with glycans either covalently or noncovalently.

5. Name some potential applications of glyconanotechnology to clinical problems.

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CHAPTER 59: GLYCANS IN BIOENERGY AND MATERIAL SCIENCE

1. What are the major uses by humans of plant glycans?

2. Discuss the positive and negative impacts of fermenting the starch present in corn grains into bioethanol.

3. What enzymes are likely required for the breakdown of biomass into sugars?

4. What chemical modifications of cellulose would lead to polysaccharide derivatives with enhanced or new properties?

5. Describe some uses for cellulose nanomaterials.

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CHAPTER 60: FUTURE DIRECTIONS IN GLYCOSCIENCES

1. Explain to a nonexpert why an understanding of glycosciences is critical to advances in the understanding and treatment of nearly every disease affecting humans.

2. Generalize about what the congenital diseases of glycosylation (CDGs) tell us about the roles of glycans in human development and biology.

3. Describe the possible future value of large-scale glycan arrays in the diagnosis of infectious diseases and in the study of other diseases.

4. Describe how advances in genomics and proteomics have accelerated progress in glycobiology.

5. At the end of this chapter there is a list of some major fundamental questions for the future of glycobiology. Can you think of at least one additional question that is not listed ?

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