The course provides the student with knowledge spanning from the fundamental theory in glycobiology to the method and technology developments for applications in bioenergy and biomaterials, biopharmaceuticals and vaccines, and healthy food. The course contains both theoretical and practical parts.

Theoretical lectures:

• Chemistry of carbohydrates, hierarchical levels of structure of sugars and glycans and their roles in complex biological systems
• Enzymes for glycan biosynthesis and nucleotide sugar enzymology
• Classification, database and mechanism of carbohydrate-active enzymes (CAZymes) for glycan degradation and modification
• Biosynthesis and biological functions of glycoconjugates in glycoproteins and glycolipids (glycosylation pathways and glyco-engineering in various organisms including plant, animal, and microbial systems)
• Applications of glycobiotechnology in food and nutrition, energy and fuels, materials, and pharmaceuticals.

Practical labs:

• Computer lab – CAZymes 3D structure/function relationship (LAB1)
• Wet lab – Demonstrate how glycoside hydrolase enzymes with different modes of action act synergistically to deconstruct a polysaccharide (LAB2)

On completion of the course, the students should be able to:

• Describe the structure of carbohydrates (mono-, oligo-, and polysaccharide) at molecular level and explain the structure–property relationship of carbohydrates at different hierarchical levels
• Describe the molecular mechanisms of key enzymes involved in the biosynthesis, modification, and degradation of carbohydrates across diverse kingdoms and compare the structure of carbohydrate-active enzymes (CAZymes)and carbohydrate binding protein in terms of their biological functions
• Using computer software tools to demonstrate the structural differences in different functional CAZymes and explain the structure/function relationship
• Design, plan and perform experiments on deconstruction and modification of polysaccharides through the combination of different CAZymes and analyze and report the results
• Describe and compare the pathways and mechanisms for the biosynthesis of glycoproteins and glycolipids and discuss their diverse biological functions
• Discuss how CAZymes and glyco-engineering can be used in industries to develop environmentally-friendly sustainable processes in food production, fuel production, materials and medical applications

Lecture 1. Course introduction and overview, and introduction and history of enzymes

Qi Zhou, Monday, 2020-03-16, 15:00-17:00

Some general important facts of carbohydrates, introduction to sustainability, comparison of enzymatic vs chemical methods, products, green chemistry, Industrial enzymes

Lecture 2. Carbohydrate structure, from monosaccharides to complex assemblies

Qi Zhou, Tuesday, 2020-03-17, 10:00-12:00

Anomer, epimer, linkage, pyranose/furanose, boat/chair, monosaccharides, disaccharides, The Fischer glycoside synthesis, polysaccharides, cellulose, starch, hemicelluloses, carbohydrate esters, wood, cell walls, little bit about cell wall glycoproteins and lignin, pectin, chitin.

Lecture 3. CAZymes

Lauren McKee, Wednesday, 2020-03-18, 10:00-12:00

CAZy classification and database, GTs - inverting and retaining mechanism, different folds. GHs - inverting and retaining mechanism, transglycosylation, endo/exo types, pockets, clefts, and tunnels, subsite nomenclature, enzyme synergy, cellulose degradation, AA-class, CAZyme modularity, how do we determine mechanisms? Lysozyme case study.

Lecture 4. Dietary glycans. Enzymes in food and biofuel production

Francisco Vilaplana, Monday, 2020-03-23, 15:00-17:00

Glycans in human diet. Simple sugars. Starch. Dietary fibres. Prebiotics and probiotics. Enzymes in food processing. Applications in starch processing, brewing and baking. Enzymes in biofuel production. Background. Biorefinery. Bioetanol 1G vs 2G.

LAB. Introduction to the wetlabs

Lauren McKee, Tuesday, 2020-03-24, 10:00-12:00

Introduction to the wetlabs, 1. Glucose oxidase assay vs DNS assay for reducing sugars, 2. Synergistic glycoside hydrolases, how endo- and exo-type glycoside hydrolase enzymes act synergistically to deconstruct a polysaccharide.

LAB. Glucose oxidase and DNS assays

Lauren McKee, Thursday, 2020-03-26, 13:00-17:00

Demonstration of techniques by video and data analysis.

LAB. Synergistic glycoside hydrolases

Lauren McKee, Friday, 2020-03-27, 08:00-12:00

Demonstration of techniques by video and data analysis.

Lecture 5. Enzymes in fiber processing

Qi Zhou, Monday, 2020-03-30, 15:00-17:00

Fungal enzymes, Application of cellulases; acivation of dissolving pulp, increase of paper strength, enzymatic deinking, Enhancing dewatering rate. Amylases, xylanase bleaching, enzymatic retting with pectinases. Plant enzymes, genomics, Case studies of in vivo OE of GA-20 oxidase, xyloglucanase, cellulase in Eucalyptus (first approved GE tree).

Lecture 6. CAZymes structure/function relationship

Christina Divne, Tuesday, 2020-03-31, 10.00-12:00

Intoduction and background to computer lab

LAB. Computer lab - CAZymes structure/function relationship

Christina Divne, Tuesday, 2020-03-31, 13.00-17:00

Looking at 3D structures different cellulases.

Övning 1. First checking point

Qi Zhou, Friday, 2020-04-03, 13:00-15:00

Lecture 7. Glycoconjugates 1

Yves Hsieh, Tuesday, 2020-04-07, 10:00-12:00

Various classes, function of glycans on proteins, N-glycosylation biosynthesis, GTs GHs, complex, hybrid oligomannose.  Introduction to lectin sorting and AB0-blood system. N-glycans and cancer, protein-protein interaction, protection against proteases, enzyme activity. Variation of N-glycsylation in various organisms (importance in recombinant protein production). Class assignment, figure out type of glycan using various inhibitors. Film about de-glycosylation

Lecture 8. Glycoconjugates 2

Thomas Crouzier, Thursday, 2020-04-09, 10:00-12:00

O-glycosylation, mucins and proteoglycans, mucins and cancer/diabetes, Glucosaminoglycans, hyaloronan, O-GlcNAc Modification, O-GlcNAc Modification and diabetes. Film of hagfish. Film about discovery of O-GlcNAc Modification. Glycosphingolipids (glycosylceramides), classes, biosynthesis, lipid rafts, neurodegenerative disorders, lysosomal disorders, receptors for bacterial toxins. Endoglycoceramidases. GPI-anchors, structure, biosynthesis, function, applications, Glycosylated sterols, lipid rafts

LAB. Feedback to wetlab reports

Lauren McKee, Thursday, 2020-04-09, 13:00-15:00

Lecture 9. Industrial production of glycoproteins

Veronique Chotteau, Tuesday, 2020-04-21, 10:00-12:00

An introduction of production of glycoproteins in industry with focus on glycosylation.

Lecture 10. Glycocongjuates in Medical applications

Yves Hsieh & Thomas Crouzier, Wednesday, 2020-04-22, 10:00-12:00

Lectin, calreticulin, L-type, P-type, C-type, R-type , mannose binding protein, mannose receptor, Asialoglycoprotein receptor, EPO, menstruation, selectins, Plant lectins, concavalin A, Ricin, bacterial toxins, bacterial and viral adhesion with lectins.

Film about ricin

The Flu, heamagglutini (H), sialidase (N), subtypes different hosts (man, pig, birds). Relenza Tamiflu (TS-analogous), risk of pandemic, discussion of man-made viruses.

Lysosomal disorders:  Fabry and Schindler diseases, enzyme replacement therapy, Active-site-specific chaperone treatment (ASSC)

Blood type interconversion, making universal blood O-group using enzymes.

Lecture 11. Seminar/Wrap up

Ines Ezcurra, All teachers, Monday, 2020-05-04, 15:00-17:00

Questions and information of the exam.

Övning 2. Second checking point

Qi Zhou, Tuesday, 2020-05-05, 08:00-12:00

Exam, Monday, 2020-06-01, 14:00-18:00

• Introduction to Glycobiology 3rd Edition (2011)
• Essentials of Glycobiology, 3rd edition https://www.ncbi.nlm.nih.gov/books/NBK310274/
• Other literature will be handed out in each theoretical lecture and practical lab

Students at KTH with a permanent disability can get support during studies from Funka:

Funka - compensatory support for students with disabilities

Please inform the course coordinator if you need compensatory support during the course. Present a certificate from Funka.

A, B, C, D, E, FX, F

• LAB1 - Laboratory course, 2.0 credits, Grading scale: P, F
• TEN1 - Written exam, 5.5 credits, Grading scale: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Examination

LAB1 – Laborationskurs/Laboratory course, 2,0 hp, P/F

TEN1 – Skriftlig tentamen/Written exam, 5,5 hp, A, B, C, D, E, FX, F

Examination elements

1. Written examination (TEN1), including Part A questions (basic questions for grade E) and Part B questions (advanced questions for higher grades, A-D)
2. Computer exercises and report (LAB1-A)
3. Written wetlab report (LAB1-B)

Assessment of Intended Learning outcomes

 Grades for Intended Learning outcomes

To achieve Grade E, the student must be able to:

• Explain and describe basic concepts regarding the main parts of the course including carbohydrate structure, carbohydrate-active enzymes, carbohydrate binding protein, enzymes in food, biofuel, and fiber processing, glycosylation and glycoproteins, industrial production and biomedical applications of glycoproteins. (examined by Part A questions in written exam TEN1 5.5 hp)
• Use the computer software and databases used in the course to visualize and compare the macromolecular structure and also perform basic analysis and evaluation of structure information and activity features of two cellulases. (examined by LAB1 2.0 hp (pass/fail))
• Apply the knowledge from the course to analyze glucose content in a pure starch sample using a commercial enzyme kit and understand the mechanism of the enzymatic reaction and compare with the chemical reducing end sugar assay. Demonstrate the ability to use the synergy of a number of enzymes to hydrolyze a complex hemicellulose by designing, planning, and performing the experiments and analyze and discussed the results. (examined by LAB1 2.0 hp (pass/fail))
• For higher Grades (A-D), deeper understanding is required in the basic parts of the course (higher scores on TEN1 part A) and that the student can also explain and compare the structure–property relationship of carbohydrates at different hierarchical levels, describe and compare reaction mechanisms of different carbohydrate-active enzymes, discuss the structure and function of carbohydrate binding modules, explain and compare the mode of action and synergy of the enzymes used in food, biofuel, and fiber processing, discuss the sustainable, environmental and social aspects for the enzymatic approach in food, biofuel, and fiber processing, explain and compare the biosynthesis pathways of N- and O-glycoproteins, discuss the function of N-glycans and the effect of glycosylation on the structure and functions of glycoproteins, explain the importance of glycosylation pattern in therapeutic drug and industrial production, describe and discuss examples of glycoconjugates in medical applications. (examined by Part B questions in written exam TEN1 5.5 hp)

Grading criteria

For grade       requirements for the student

E                      i) The student can explain and describe basic concepts regarding the main parts of the course including carbohydrate structure, carbohydrate-active enzymes, carbohydrate binding protein, enzymes in food, biofuel, and fiber processing, glycosylation and glycoproteins, industrial production and biomedical applications of glycoproteins. (pass for Part A questions in written exam TEN1 5.5 hp)
ii) The student is able to use the computer software and databases used in the course to visualize and compare the macromolecular structure and also perform basic analysis and evaluation of structure information and activity features of two cellulases. (pass for LAB1 2.0 hp)
iii) The student can apply the knowledge from the course to analyze glucose content in a pure starch sample using a commercial enzyme kit and understand the mechanism of the enzymatic reaction and compare with the chemical reducing end sugar assay. The student can demonstrate the ability to use the synergy of a number of enzymes to hydrolyze a complex hemicellulose by designing, planning, and performing the experiments and analyze and discussed the results. (pass for LAB1 2.0 hp)

D                   In addition, the student can perform in greater detail in several parts of the course contents including explain the structure–property relationship of carbohydrates at different hierarchical levels, describe reaction mechanisms of different carbohydrate-active enzymes, describe the structure of carbohydrate binding modules, explain the mode of action of the enzymes used in food, biofuel, and fiber processing, explain the biosynthesis pathways of N- and O-glycoproteins, explain the importance of glycosylation in therapeutic drug, describe examples of glycoconjugates in medical applications. (higher points in Part A questions and 30% points in Part B questions in written exam TEN1 5.5 hp)

C                   In addition, the student can perform in greater detail in most parts of the course contents listed in grade D. (more points in Part B questions in written exam TEN1 5.5 hp)

B                   In addition, the student can perform in greater detail in most parts of the course contents including compare the structure–property relationship of carbohydrates at different hierarchical levels, compare reaction mechanisms of different carbohydrate-active enzymes, discuss the structure and function relationship of carbohydrate binding modules, compare the mode of action and synergy of the enzymes used in food, biofuel, and fiber processing, discuss the sustainable, environmental and social aspects for the enzymatic approach in food, biofuel, and fiber processing, compare the biosynthesis pathways of N- and O-glycoproteins, discuss the function of N-glycans and the effect of glycosylation on the structure and functions of glycoproteins, explain the importance of glycosylation pattern in industrial production of glycoproteins, discuss examples of glycoconjugates in medical applications. (higher total points in Part A questions and more points in Part B questions in written exam TEN1 5.5 hp)

A                   In addition, the student can perform in greater detail in all parts of the course contents listed in grade B. (higher total points in Part A questions and higher total points in Part B questions in written exam TEN1 5.5 hp)

The written exam

The examination of BB2425 Glycobiotechnology will be carried out via Zoom and Canvas. The examination is divided in two sessions (1.5 hour each).

• The exam consists of 7 questions with 100 total points covering the 7 topics including carbohydrate structure, carbohydrate enzymology, enzymes in food and biofuel, enzymes in fiber processing, glycoconjugates, industrial production of glycoproteins, glycoconjugates in medical applications.
• Each question consists of 2-6 sub-questions with 1-3 questions belong to Part A (basic questions for grade E) and 1-3 questions belong to Part B questions (advanced questions for higher grades, A-D).
• The total points for Part A questions is 50. The total points for Part B questions is also 50.

Grading requirements

A pass grade of at least 35 points is required for part A of the written exam (TEN1). For higher grades, an increasing proportion of points are required to be collected at both part A and part B questions.

For grades             Required

E                                 Pass

D                                Pass and at least 50 points in total

C                                 Pass and at least 60 points in total

B                                 Pass and at least 70 points in total

A                                 Pass and at least 85 points in total

• All members of a group are responsible for the group's work.
• In any assessment, every student shall honestly disclose any help received and sources used.
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.