Course content

This course covers primarily chemical kinetics and thermodynamics applied to biomolecules, including analytical techniques. It serves to lay groundwork for future studies in our undergraduate Bioengineering curriculum.

There is no required text for the course, but the following texts are particularly useful.

The Molecules of Life, by Kuriyan, Konforti, and Wemmer
Quantitative Fundamentals of Molecular and Cellular Bioengineering, by Wittrup, Tidor, Hackel, and Sarkar

You are strongly encouraged to acquire both of these books. Additionally, Molecular Driving Forces by Dill and Bromberg is a good resource. The out-of-print book Physical Chemistry with Applications to the Life Sciences by Eisenberg and Crothers is also a good, more detailed reference. All four of these books are available on reserve at the Caltech library.

Meetings

Most of the course material will be delivered in lecture, held Tuesdays and Thursdays, 9-10:30 am PST, in Broad 100. Attendance at lecture is mandatory. Please make every effort to come to class.

Lectures are a very important time for me to interface with you. As we have discussions in lecture, we both learn, and I get a good idea of how you are doing with the material. I therefore often find it distracting when students use laptops in lecture. Therefore, no laptops are allowed in lecture. Tablets may be used only for notetaking purposes and cell phones must be completely silenced and put away.

I also strongly recommend you attend instructor and/or the TA office hours.

Homework

We will have roughly weekly homework assignments. They serve to provide practice and reinforcement of the content discussed in lecture. There may be some problems that do not have "right answers," but are aimed at making you think about the central concepts of the course. Following are homework policies.

Homeworks are submitted as hard copies in lecture on the due date. You will lose points for illegible homework. If you write on a tablet or type your homework, you need to submit a printout. There is a printer available in B131 Kerckhoff for you to use for this purpose if you wish.
Mathematical expressions must be clearly presented with all variables defined.
Homeworks have a specified due time, usually at the start of lecture on Thursdays. You are expected to turn homework in on time. No late homework will be accepted with exceptions outlined below.

You have a total of six "grace days" you can use throughout the term. If you use grace days, your homework may be submitted late without penalty. A grace day is spent for each 24 hours, or portion thereof, that a given homework is late. For example, if a homework is due at 9 AM on Thursday, but you turn it in at noon on Saturday, you spend three grace days, the first one being spent at 9 AM on Friday, the second at 9 AM on Saturday, and the third for the remaining three hours on Saturday. After you spend six grace days for the term, no late homeworks will be accepted.
To submit at late homework, you may either hand it directly to a TA or put it in the instructor's mailbox in the Administration room on the ground floor of Broad. In either case, you must post a contemporaneous private Ed note with the time of submission. If you are submitting on a weekend or evening when a TA is unavailable and you do not have access to Broad, you may include photos or a scan of your completed homework in the private Ed note and submit the homework as soon as a TA is available or Broad is unlocked.
If you have an extended illness requiring you to spend more than six grace days, you need to provide a note from a health care provider.
If you have a CASS accommodation, you need to communicate it to the instructor within the first week of class. If your accommodation allows for extra time on coursework, you need to let the instructor know you will be exercising that accommodation at least 24 hours before the homework is due.

You may not refer to homework problems from previous editions of this course (including under its former names of Ch 25 and BE 25). You also may not refer to solutions manuals, etc., for problems assigned from textbooks. If you come across a solution to a problem identical or very similar to the one assigned, you cannot refer to that solution.
You may not use chatbots, large language models, or any other artificial intelligence for coursework.
In general, "homework by Google" is ill-advised. Slogging through a tough problem is often the best way to learn a concept, which is the whole point of the homework. If you do find a resource that helps you (i.e., not something that just gives the solution) with your assignment, provide a citation of that resource.
You are welcome, and even encouraged, to work with your classmates on your homework. Note that Ed is a valuable resource to discuss the homework with the course staff and with your classmates. If you do work with a classmate or classmates, please indicate with whom you worked in your homework submission. In all cases, the work should be substantially your own, and you should have full mastery of whatever you submit. You may not copy solutions from classmates.

Exams

There will be two exams, a midterm and a final. Details about the exams will be available close to when the exams are released. They will most likely be oral exams in the following format: You will have one hour to work on problems immediately before a half-hour in-person presentation of your solutions. Grace days may not be applied to exams. If you need special arrangements for exams for health or other reasons, please contact the course instructor as far in advance as possible, and no later than one week before the exam.

Grading

Your grade will be determined as follows.

50% homework
20% midterm
30% final

For any regrade requests, the entire assignment or exam may be regraded.

Course communications

Use the class Ed page for questions related to course topics and homework. Almost all of our mass communication with you will be through Ed, so be sure to set your Ed account to give you email alerts if necessary. You should use Ed for all communications except for issues of a personal nature, such as excuses for illness, in which case you should contact the course instructor directly via email.

Ediquette

When posting on Ed, please follow these guidelines:

Your public posts should serve to help clarify concepts or ask about general directions. If you have specific questions that require showing much of your solution to a homework, make the post private, viewable only to the course staff.
We will not be writing much computer code, but if you have a question about a coding bug make every attempt to provide a minimal example that demonstrates the problem. A minimal example strips out all other details beyond what is necessary to reproduce the problem or bug. Posting error messages without code is seldom helpful.
While you are free to post anonymously to your classmates (course staff will always know who posts), we encourage you to post with your real name. This can spur discussions among students, which can be productive. This also spurs more conversation and results in faster answers to questions.