Overview

Description

CALENDAR DESCRIPTION:

An advanced, in-depth treatment of a specialized area of organic chemistry.

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:

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

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:

RECOMMENDED READING: