Spring 2021 - CHEM 759 G200

Special Topics in Organic Chemistry (3)

Chemical Biology

Class Number: 8191

Delivery Method: Remote

Overview

  • Course Times + Location:

    Mo, We, Fr 12:30 PM – 1:20 PM
    REMOTE LEARNING, Burnaby

Description

CALENDAR DESCRIPTION:

An advanced treatment of specific topics related to the study of organic compounds. Topics which will be discussed will vary from one term to the next.

COURSE DETAILS:

Please note, this course outline was accurate at the time of publication but is subject to change.

Mode of Teaching:
3 lecture hours/week; 1 tutorial hour/week
Lecture: Synchronous
Tutorial: Synchronous

Course description: 
This modular survey course will introduce students to modern topics in chemical biology with an emphasis on applications of organic chemical principles to biological research and biotechnology.  The course is divided into three modules as follow:

Module 1 – Introduction to chemical biology – synthesis, biosynthesis, and unnatural of biomolecules
Module 2 – High throughput methods in chemical biology – chemical genetics
Module 3 – Imaging life using chemical biology – fluorescence and other methods

The topics to be covered in the lectures will include an overview of the major classes of biomolecules (nucleic acids, proteins, carbohydrates) from the perspective of chemical biology. Examples of chemical probes used in imaging, chemical genetics, and emerging methods for manipulating the levels and activities of biomolecules will be described. Examples of major experimental advances accomplished using these methods and tools will be noted with an emphasis will be placed on current and classic papers in the primary literature as well as critical review of recent research papers. Though not required, owing to the interdisciplinary nature of the subject matter of this course, students will benefit from an introductory-level understanding of biochemistry as well as cell and molecular biology.

Topics covered in each course module:  

Module 1: Introduction to chemical biology – synthesis and biosynthesis of biomolecules

  1. What is chemical biology?
    • General structure of cells and cell theory
    • Introduction to cell cycle
    • Transient interactions enable biology
    • Revisiting the central dogma of molecular biology
  2. Chemical biology of nucleic acids
    • Structure and properties of DNA and RNA
    • Revisiting replication and transcription
    • Roles of synthetic DNA in molecular biology
    • Introducing unnatural nucleobases into nucleic acids
  3. Chemical biology of proteins
    • Amino acids and proteins – structures and properties
    • Introduction to translation
    • Post-translational modifications
    • Methods to synthesize peptides and unnatural proteins
  4. Chemical biology of glycoconjugates
    • Structure and properties of glycoproteins and glycolipids
    • Biosynthesis of glycosidic linkages
    • Methods to globally manipulate glycans
    • Chemical synthesis of oligosaccharides

Module 2 – High throughput and other enabling methods in chemical biology

  1. Developments in DNA sequencing
    • Dideoxy sequencing
    • Next and Third Generation sequencing methods
    • Select uses of DNA sequencing in directed evolution, biology, and DNA encoded libraries
  2. Strategies and concepts for molecular evolution
    • Introduction to combinatorial strategies to identify new molecular properties
    • Selections and screens
    • Directed evolution in vitro and in vivo
    • DNA templated libraries
  3. Chemical approaches to identifying targets and gene function
    • Forward and reverse chemical genetics – target based and phenotypic screening
    • Combinatorial libraries, DNA encoded libraries, Diversity Oriented Synthesis (DOS)
    • Methods for target identification
    • Linking gene to gene function using chemical tools
    • Methods for controlling proteins using small molecules

Module 3 – Imaging life using chemical biology

  1. Introduction to detecting biomolecules in cells and in vivo
    • Basic principles of fluorescence
    • Overview of basic fluorescence imaging methods
    • Luminescence
  2. Detecting biomolecules in cells using chemical biology
    • Proteins – genetically encoded fluorescent tags and small molecule labeling methods
    • Nucleic acids – genetically encoded tags and small molecule labeling methods
    • Glycans – metabolic engineering and small molecule labeling methods
  3. Detecting small molecules and enzyme activity in cells using chemical biology
    • Enzyme substrates, activity based proteomic probes, genetically encoded sensors
    • Improved fluorophores, quantum dots, nanoparticle quenching
    • Super resolution microscopy
    • Small molecule sensors

COURSE-LEVEL EDUCATIONAL GOALS:

Expected outcomes: Students will learn to read and critically analyze scientific papers in chemical biology. Students will learn the current state of the field of chemical biology. Students will learn how other fields in chemistry impact and enable chemical biology research. Students will learn how chemical biology is an enabling field for academic and industrial research.

Literature discussions and presentations:
 The reading of scientific literature is an essential skill for scientists in all sectors; government, private, and academic. One aim of this course will be to improve skill at reading the literature through practice and discussion. Classes will therefore involve discussion of assigned literature during tutorials. Prior to class discussion students will prepare a concise write-up on the assigned questions. During class discussion we will briefly analyze the assigned paper and evaluate connections to the lecture material. Each student will also present a current paper from the chemical biology literature with approval from the instructor, summarizing the work, defining the key advances, and outlining the signficance of the work for the wider field.

Grading

  • Discussion Write-ups and Participation 35%
  • Short Problem Sets 15%
  • Presentation 20%
  • Module Quizzes 30%

NOTES:

Online Exam Invigilation: Students completing exams remotely must comply with the online invigilation procedures implemented by the course instructor.

Materials

MATERIALS + SUPPLIES:

Technology Requirements: Students are required to have a desktop or laptop computer, high-speed internet access, and a webcam and microphone (built-in or external) to participate in online courses.

REQUIRED READING:

Lectures will be based largely on the primary literature and the following text by Profs. Van Vranken & Weiss at UC Irvine:     

  • Van Vranken, D. L. & Weiss, G. A. Introduction to Bioorganic Chemistry and Chemical Biology

RECOMMENDED READING:

Additional reading is recommended for students with limited background in introductory biochemistry, biological chemistry, and molecular and cell biology. The following books are either available on-line at the PubMed bookshelf or have been requested to be on reserve in the Bennett library.  Some can be found on the PubMed bookshelf (online).  

  • Alberts, B. A., et al.  Molecular Biology of the Cell (4th edition and onward).
  • D. Voet and J.G. Voet, Biochemistry, (3rd edition and onward).
  • Blackburn, G.M & Gait, M.J. Nucleic Acids in Chemistry and Biology (2006 edition)            
  • Varki, A., et al. Essentials of Glycobiology, (2009) (available on-line)

Graduate Studies Notes:

Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.

Registrar Notes:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

SFU’s Academic Integrity web site http://www.sfu.ca/students/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html

TEACHING AT SFU IN SPRING 2021

Teaching at SFU in spring 2021 will be conducted primarily through remote methods. There will be in-person course components in a few exceptional cases where this is fundamental to the educational goals of the course. Such course components will be clearly identified at registration, as will course components that will be “live” (synchronous) vs. at your own pace (asynchronous). Enrollment acknowledges that remote study may entail different modes of learning, interaction with your instructor, and ways of getting feedback on your work than may be the case for in-person classes. To ensure you can access all course materials, we recommend you have access to a computer with a microphone and camera, and the internet. In some cases your instructor may use Zoom or other means requiring a camera and microphone to invigilate exams. If proctoring software will be used, this will be confirmed in the first week of class.

Students with hidden or visible disabilities who believe they may need class or exam accommodations, including in the current context of remote learning, are encouraged to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112).