University of Washington CSE 599 - Biochemistry for Computer Scientists

Course Logistics

First class: Tuesday October 1, 2013. 10:30 - 1:20.

Location: CSE 503

Meets weekly at same time and place

Instructor: Joseph L. Hellerstein, Google, Seattle, WA.

email: jlh@google.com


Course Objectives

The advent of inexpensive DNA sequencing technology has created an explosion of opportunities in the science and engineering of life processes. Training for these opportunities requires a blend of biochemistry, statistics, and computer science. Some effort has been devoted to training biochemists in software engineering. This course is about educating computer scientists in biochemistry to promote interdisciplinary work between computer science and biochemistry.


The course provides CS students with an introduction to the basics of biochemistry. The focus is on enzymes and their actions in the "central dogma" of biology - DNA replication, transcription, and translation. With this background, student should be able to address problems such as analyzing the effects of DNA mutations on (protein) translation as well as interpret laboratory data from DNA sequencing. The scope and content of this class is also described in this University of Washington eScience seminar.


Mechanics

The class meets once a week for three hours. The first nine classes will be lectures. The lectures will include mini-problems that test knowledge of the material, and there will be a longer problem (~20 minutes) that is solved as a group at the end of the lecture. The course includes a programming project using publicly available databases. The last class will be presentation of student projects. Students will be required to attend at least one biochemistry research seminar and provide a short summary of the material presented.

Pre-requisites

  • Science: general chemistry, general biology.

  • Software skills: python, javascript, software version control (e.g., git), database systems

Syllabus by lecture


1. 10/01: Course overview and biology basics.

    1. Course overview (biology and nanotechnology as biochemistry; cell components and cell chemistry)

    2. Lecture: Core concepts in biology - cell structure, life cycles, tree of life, central dogma.

    3. Lab: Web Applications. javascript and javascript development tools.

2. 10/08: Chemistry for computer scientists.

    1. Lecture: essentials from general chemistry (orbitals, bonds) and key elements of organic chemistry (line drawings, reaction mechanisms). UML representation of chemical structures and reactions.

    2. Lab: Introduction to ChemDoodle and iChemLab web components.

3. 10/15: Protein structure and function

    1. Lecture: Amino acids. Protein primary, secondary, tertiary, and quaterinary structure. Mechanisms for hemoglobin and aspartate transanimase

    2. Lab: Case study of bonds for protein folding in ChemDoodle

4. 10/22: Enzymes
    • Lecture: Activation energy, nature of biological catalysts, models of enzyme mechanisms, active site, regulation site, metrics for enzyme effectiveness, inhibition. Simple examples from glycolysis.
    • Lab: Analyzing enzyme metrics

5. 10/29: Central dogma of biology I. Replication.

    • Lecture: DNA structure. Replication overview and key enzymes.

    • Lab: Aligning sequencer reads to a reference genome.


6. 11/05: Biochemistry data resources

7. 11/12: Central dogma II. Transcription and Translation.

    • Lecture: mRNA, splicing, editing. Mechanism for producing proteins. Effects of DNA mutations.

    • Lab: Protein databases and protein analysis; parsing protein molecules


8. 11/19: DNA sequencing and measuring protein expression

    • Lecture:

    • Lab: Modeling signaling as data flows that transform enzymes


9. 11/26:Class is cancelled.


10. 12/3: Course summary and student presentations.

Course Materials


(last updated: November 1, 2013)