USMx: BIF002x Proteins: Alignment, Analysis and Structure

Syllabus

Proteins: Alignment, Analysis and Structure

Course Dates: Aug 21st – Oct 16th 2017

Course Description

Proteins play a very important role in all organisms. In fact, most of the work that happens inside every cell happens because a specific protein is employed for a specific task. Often the three-dimensional shape of a protein plays a major role in its function. As such, it is important to know the structure of all proteins to have an idea of what function they perform.

One of the jobs of a bioinformatician is to predict the three-dimensional structure of a protein using only the DNA sequence that encodes it as well as determining the effects of any mutations in the DNA on the three-dimensional structure/function.

In this course, part of the Bioinformatics MicroMasters program, you will learn about protein structure and its impact on function, practice aligning protein sequences to discover differences, and generate model structures of proteins using web and software-based approaches. 

Course Learning Outcomes

In this course, which is a part of the Bioinformatics MicroMasters program, you will learn the following:

• The different types of protein structures: primary, secondary, tertiary & quaternary
• Gene expression from DNA to amino acids
• Different types of EC codes
• Features of Structural and Cell Skeleton proteins
• Functions of Adhesive and Cell Motor proteins
• Process of Glycosylation
• Processes involved with chromatography and spectroscopy
• Different aspects of X-Ray diffraction, electron microscopy, protein structure prediction and splicing
• Various steps involved in enzyme kinetics, protein-protein interaction networks and Proteomics

Course Information

This is a self-paced online course. All course materials are presented in English.  Learners new to edX are recommended to take the DemoX course, which is designed to show new students how to take a course on edx.org. 

Course Materials

All materials are freely available within the course. Additional references, resources, and optional readings can be easily accessed and downloaded from the References, Resources, and Optional Readings sections of this course. 

Course Schedule

The course will open on Aug 21, 2017 and run for eight weeks. As this is a self-paced course, all content will be available in Week 1 including weekly knowledge checks and discussions. The course ends Oct 16, 2017. Students should plan to spend between 4-6 hours each week to fully complete each module.

Week	Topics	Optional Reading	Activities
1	Introduction to proteins Transcription and Translation Protein Structure	Amino Acid Structures	Week 1 Discussion Week 1 Knowledge Check
2	Glycolysis EC Codes & Structural Proteins Enzymes & Diseases	Glycolysis	Week 2 Discussion Week 2 Knowledge Check
3	Adhesive Proteins Cell Motor Proteins Transmembrane Proteins	BSCB Membrane Proteins Glycosylation	Week 3 Discussion Week 3 Knowledge Check
4	PAGE, Protein Blots & ELISA Chromatography & Spectroscopy Protein Sequencing & Analysis	Protein Purification Practical Application of Protein Identification	Week 4 Discussion Week 4 Knowledge Check Midterm Assessment
5	Multiple Sequence Alignments Protein Domains Phylogenetics	Protein Domain/Motif  Protein Domain Evolution	Week 5 Discussion Week 5 Knowledge Check
6	Protein Structure Prediction Protein Function Prediction Protein Docking Prediction	Protein Structure Prediction  Protein Docking	Week 6 Discussion Week 6 Knowledge Check
7	Protein Modification Protein-Protein Binding Protein-NA Binding	Post Translational Modification Hidden Markov Models	Week 7 Discussion Week 7 Knowledge Check
8	Enzyme Kinetics Protein-Protein Interaction Networks Proteomics	Enzyme Kinetics  Proteomics	Week 8 Discussion Week 8 Knowledge Check Final Assessment

Course Grading and Policy

You will be able to view all material and take any knowledge checks, or participate in discussions at any time during the course. However, to be awarded a certificate you will need to have completed all the assessments, discussions and knowledge checks by the last scheduled date for the course.

The course score for BIF002x is determined from two components: a Mid Term Assessment (50%) and a Final Assessment (50%).

Mid-Term Assessment

At the end of the material for Week 4, there is Mid-Term assessment, which accounts for 50% of your overall score in the course. The Mid-Term contains 25 randomly generated questions based on the topics covered from Week 1 to 4. These questions are multiple choice and are two points each.  Note: you will only have one attempt at this assessment.

Final Assessment

At the end of the material for Week 8, there is a Final assessment, which accounts for 50% of your overall score in the course. The Final assessment contains 25 randomly generated questions based on the topics covered from Week 5 to 8. These questions are multiple choice and are two points each. Note: you will only have one attempt at this assessment.

Certification

For those students working to obtain the MicroMasters certificate, you must register for the verified track before the deadline and obtain a total score of 80% or greater in the class. For those verified students who receive an edX certificate, it will appear on their edX dashboard after the course ends. As of December 7, 2015, edX no longer offers certificates for students who audit a course.