Department of Biology, UCSD
BIMM 100
Molecular Biology
Fall, 2000
M W F, 10:10 - 11:00 pm ... York 2722
| BIMM100 | Syllabus
| Sections / Off Hrs | Grading
Policy | DNASYSTEM
|
| Lectures | Journal
Articles | Study Qs | Lab
Techniques | Exams |
Instructor:
Grad Teaching Assistants:
Undergrad Teaching Assistants:
Topics for this main BIMM100 Web Page:
- The Course - Learning Molecular Biology
Genome Emphasis of the Course
How to Study for this Course
General Information
BIMM100 Web Pages
News and Announcements
The Course - Learning Molecular Biology
Grades are based on Two Midterms, held Tuesday
evenings with unlimited time, and a Final Exam, plus TA
input for borderline cases (see end of the Syllabus
Web page).
Grades are given only at the end of the course, and are largely
based on a 'curve'.
Plus and minus Grades will be given.
Exams are based mainly
on Lecture Notes and Journal Article readings, with supplementary
material from the textbook assigned readings. Exams sometimes
expect you to apply concepts and principles to new situations.
However, any new situations or concepts that you may see
on exams you should be able to figure out from what is present
in the Lectures, in the Textbook, and in the Journal Articles.
For Exams, you are responsible ONLY for material presented
in lecture, present in Lecture Notes on the Web, assigned readings
in the required text (Brown, "Genomes"), and material
presented in the assigned Journal Article readings, and for any
new situations that are based on these materials.
In particular, you are NOT responsible for material presented
previously in this course but not presented this year, or for
material presented in the recommended textbook (Voet-Voet, "Biochemistry")
not presented in class.
Genome Emphasis of the Course
The official Textbook is Brown, "Genomes".
This new textbook presents molecular biology from the viewpoint
of entire genomes rather than gene by gene. This new viewpoint
reflects recent and revolutionary advances in genomics and experimental
methodologies arising from the human genome project and the sequence
information from model organisms.
One result of this change in viewpoint from genes to genomes
is that the Lectures will be substantially new and different for
this course. Lecture Notes previously used will thus not
be available on the Web. However, new Lecture Notes, as they are
written, will be made available on the Web under Lecture
Notes.
Lectures will be based on the assigned readings in Brown, and
some Brown figures will be shown as overheads in class. Some other
figures may also be used, for example, from Voet and Voet, "Biochemistry",
as supplements. In such case, copies of these figures will be
posted on this Web site for your examination.
Any standard Molecular Biology or Biochemistry text will provide
you with much of the course information. In this regard, Voet-Voet,
"Biochemistry", 2nd edition, is a "recommended"
text for this course, and the course Syllabus contains general
chapter references to comparable lecture material this book. The
Syllabus also lists a few other standard textbooks. All of these
textbooks are on reserve in the Biomedical Library for this course.
However, NONE of these standard textbooks treat Molecular Biology
specifically from a genome viewpoint.
How to Study for this Course
Students often ask how they should study for this course.
My response is usually a rather general one, as follows:
The important point is to learn the concepts, principles,
and specifics covered in lecture, in the assigned textbook readings,
and the main points in the assigned Journal Articles.
By 'learning' this material is meant: how much you have
assimilated into your brain, how much you can include in answers
to questions about the material WITHOUT looking at notes or other
written material.
Given this, how do you get the stuff into your brain? and
how do you know that you have done this once you think you have
done it?
The best way: once you think you know some of the material,
go off by yourself and attempt to answer questions about the material.
Do this 'from memory'. Think about the material as though you
were giving a lecture on the material. Consider yourself to be
a TA and you are answering questions from students in Section;
consider that you are attempting to 'clarify' material that is
confusing to a student in your section.
When you do this, you will find that it is difficult. You will
find that you don't really yet know the material 'by heart'. You
need then to go back to your Lecture Notes and other stuff, and
clarify what you didn't yet know. And then try again.
Function of the Lecture Notes: Although Lecture Notes
will NOT be available from Soft Reserves this year, I hope to
have the revised Lecture Notes posted on the Web before presentation
in class. If so, you can look at the Lecture Notes before
class, to improve understanding of the material during class.
You would then also have the opportunity to print out the lecture
notes from the Web pages, bring a copy to class, and simply 'supplement'
or 'annotate' the Lecture Notes with your additional notes from
lecture.
Note the following!!
Students also will often spend a lot of time on the lecture
notes they took during class. They will rewrite them, they will
underline them, they will highlight them, etc etc.
This is not the final goal! It does NO GOOD during exams
to have beautiful lecture notes but little information in your
brain. Lecture notes, the textbooks, all of this material is a
means to an end, the end being how much you have in your brain!
Hence, the main thing you want to do is:
1. do what you need to do to get the material into your brain
2. do what is needed to convince yourself that you do in
fact have the material in your brain
One final point: exams. Every instructor has their own
'style' for exams. Once you have learned the material, you still
need to demonstrate this by doing well on the exams. To learn
how to do well on Smith exams, do the following:
- Look at old exams posted on the Web.
Think of similar questions when you are convincing yourself that
you have learned the material.
- Look at the answers given in the keys.
This will give you some idea of the nature of the answer expected
from the questions asked.
- When taking an exam, read the question before answering
the question!
This means understanding what is being asked !
... and answering ALL parts of the question!
If you don't understand what is being asked for during an exam,
raise your hand and ask for clarification.
If you learn the material covered in lectures, the assigned
textbook readings, and the main points in the Journal Articles,
you will get an A in the course.
General Information
All information for BIMM 100 is available on the following
Web pages
Bad or Missing Web Links ?? ... please send email to
D. Smith
Course Materials:
Soft Reserve Readers: A BIMM 100 Course Reader will
be available from Soft Reserves sometime during the first week
of classes that contains:
Study Questions: the Study Questions in the Soft Reserves
Course Reader are based on this course as previously taught!
Although there will be a significant overlap between the previous
material and the material this year, there will be material in
the Study Questions that will not be covered this year,
and there will be new material this year not covered in the Study
Questions found in the Course Reader.
Discussion Sections and Office Hours: see Sections
/ Off Hrs
- You are welcome to go to any, all, or none of the Discussion
Sections.
- Input from TAs is sometimes important in determination of
final grades in the course in the case of borderline situations.
A Journal Article Discussion Section will
be led by D. Smith which will focus on discussion of the assigned
Journal Articles. This will probably be on Thursdays at 3:30 pm;
see Sections / Off Hrs for details.
Exams and Grades: see Syllabus
and News and Announcements for information
- Grades are assigned only at the end of the course, and are
based on two Midterms and a Final Exam.
- In cases of poor performance on one Midterm relative to the
other, the poor Midterm is discarded ... see Grading
Policy
- Exams are based primarily on Lecture material, supplemented
with Text readings and assigned Journal Articles. The style of
the exams is mainly "short answer" ... for sample exams,
see Exams
First Midterm: The First Midterm covers material up
to the Wednesday prior to the First Midterm. The precise "stop
point" will be announced in class.
Second Midterm: The Second Midterm covers material from
the end of material covered on the First Midterm up to the Wednesday
prior to the Second Midterm. The precise "stop point"
will be announced in class.
Final Exam: The Final Exam covers the entire Course,
with about a 2-fold emphasis on material covered since the Second
Midterm.
Questions or Confusions ?? send email to D.
Smith
BIMM100 Web Pages
BIMM100 - This Web page
of general information for BIMM 100, Molecular Biology, Winter,
2000
Syllabus - Course Syllabus
... contains any Changes made since the Course Reader went to
press.
Sections / Off Hrs - Times,
Places, Instructors for Lectures, Discussion Sections, and Office
Hours
Journal Articles - Citations
for the 6 Journal Articles and tips for reading the articles.
Lectures - Updated
versions of Lecture Notes
Grading Policy - Three step
procedure used for dropping one Midterm and calculating Total
Course Score and Grade.
Study Questions - Questions
on Lecture, Text, and Journal Article materials.
Lab Techniques - A series
of Web pages on Molecular Biology lab techniques, created by Hooman
Rashidi, Grad TA, 1997, from other Web pages.
Exams - Sample exams from past
years, as well as posted Keys for this course, Winter, 2000.
DNASYSTEM
- DNASYSTEM Home Page of Web sites for Genomics and Informatics
... Smith research interests
News and Announcements - Last Updated Saturday,
16 December, 2000
Saturday, 16 December, 2000:
- The Final Exam
has been graded and the Grade Distributions
have been determined and submitted.
- Exams with signed waivers are available in the hall
outside of Smith's office, 5254 Muir Biology Building.
- Exams with unsigned waivers may be picked up from
Smith next quarter or at a time arranged via an email message.
- The Final Exam Key is posted outside Smith's office
and can also be found here.
- The Final Exam Distribution is posted outside Smith's
office and can also be found here.
- The Total Score and Grade Distributions are posted
outside Smith's office and can also be found here.
Friday, 1 December, 2000:
- Lecture 29 (last
lecture) has been modified to remove material not discussed in
lecture.
You are responsible only for the material in this modified lecture,
namely, Lander's 10 Goals
- For those interested in a more complete Introduction to Bioinformatics,
check out the lecture here.
Wednesday, 29 November, 2000:
- TAs are needed for BIMM 100, Winter, 2001!!
If you are a good student and wish to do this, go to the Student
Affairs office in Pacific Hall, First Floor.
- Smith Office Hrs, Wednesday, 29 November: 3:15 - 4:15 pm
- Smith Office Hrs, Thursday, 30 November: 2:30 - 4:30 pm
- J. Article Six will be discussed in J. Discussion
Section, Thurs 30 Nov, 4:40 - 5:30 pm, Solis 107
- The figures from Journal Article Six are much better
when visualized in color.
These figures are now available here.
- Final Exam will be Friday,
8 December, 2000, 8:00 - 11:00 am (fixed 3 hrs time)
- The exam will be held in York 2722
- The Exam will cover the entire course, with a 2:1 emphasis
on material since the Second Midterm
- All Journal Articles will be covered
- No calculators will be permitted
- Smith will have extended Office Hours next week, to
be announced
- Review Session: The TAs will have a question/answer
(non-lecture) Review Session as follows:
- Tuesday 5 December, 7 - 9 pm, 1103 Muir Biology Building.
Monday, 27 November, 2000:
Wednesday, 15 November, 2000:
- Lecture 24,
on Genetic Codes, has now been updated.
- Lecture 25, on the Components
(tRNA, Ribosomes) of Genome Translation (Protein Synthesis),
has now been updated.
- Lecture 26, on the Process
of Genome Translation (Protein Synthesis), has now been updated.
Monday, 13 November, 2000:
- The key for Midterm 2 is now
available here; statistics are available
here.
- The key will also be available in Soft Reserves late on Tuesday,
14 November, 2000.
Sunday, 12 November, 2000:
- Lecture 21,
on Eukaryotic RNA Processing, has now been updated.
- Lecture 22, on Eukaryotic
RNA Splicing, has now been updated.
Wednesday, 8 November, 2000:
- Lecture 20,
on Eukaryotic Gene Regulation, has now been updated.
Tuesday, 31 October, 2000:
- Lecture 17,
on Prokaryotic RNA Transcription, has now been updated.
- Lecture 18,
on Prokaryotic Transcription Regulation, has now been updated.
- Lecture 19, on Eukaryotic
RNA Transcription, has now been updated.
- Midterm 2 will be next Tuesday,
7 November, 2000, beginning at 7 p.m. (unlimited time)
- The exam will be held in Centre 113 and Centre 115
- Students with last names beginning with A through M,
please go to Centre 115
- Students with last names beginning with N through Z,
please go to Centre 113
- The Exam will cover material covered in Lecture up through
Friday, 3 November, 2000
- Journal Articles 3 and 4 will also be covered on this Midterm
- No calculators will be permitted
- Smith will have extended Office Hours before the Midterm
1:
- Monday afternoon, 1 pm - 4 pm; Tuesday all day, 9 am -
4 pm
- Review Session: The TAs will have a question/answer
(non-lecture) Review Session as follows:
- Sunday 5 November, 5 - 7 pm, 1103 Muir Biology Building.
- Journal Discussion Section 4, for this Thursday,
2 November, 2000, has been cancelled,
due to another meeting for Smith.
- You are nevertheless still responsible for the subject matter
of this Journal Articles 4, three short review articles
on DNA Repair, since most of the material was covered either
in Brown or in lecture.
Wednesday, 25 October, 2000:
- Lecture 16, on Homologous
Recombination, has now been updated.
- Lecture, Friday 27 October, on Homologous Recombination
("Lecture 16"):
Smith will be out of town on Fri 27 Oct, and the lecture
will be presented by one of the Graduate TAs,
Emily Barria, as Guest Lecturer. The lecture will cover
material on Homologous Recombination (Lecture
16)
Friday, 20 October, 2000:
- Lecture 11, on DNA Replications
Basics, has now been updated.
- Lecture 12, on DNA Replication
Initiation and Elongation, and Lecture
13, on DNA Replication Termination and Telomeres, are now
(Fri, 20 Oct, 8 pm) also available.
- Lecture 15, on DNA Mutations
and DNA Repair, has now been updated.
- The material for "Lecture 10" and "Lecture
14" will be incorporated into other lectures.
- Midterm 1: The midterms are
now available ...
- If you signed the waiver, you can pick up your exam from
the floor outside Smith's office, 5254 Muir Biology
- If you did not sign the waiver, you can pick up your exam
after class from Smith.
- Be sure to check the addition on your exam !?!
- The key is posted outside Smith's office, is available
at the BIMM 100 Web site here, and
will be available in Soft Reserves by Tuesday 24 October,
2000.
- Regrades: to have your Exam regraded, write the parts
of the exam you wish regraded on the cover page, and give the
Exam to Smith, either directly or by sliding it under his office
door (5254 Muir Biology).
Note: Smith has the option to regrade the ENTIRE exam
in regrades!!! He does NOT do this for addition errors.
- Lecture, Monday 23 October, on DNA Repair ("Lecture
15"):
Smith will be out of town on Mon 23 Oct, and the lecture
will be presented by one of the Graduate TAs,
Nikki Freed, as Guest Lecturer. The lecture will cover
material on Mutations and DNA Repair (Lecture
15)
Thursday, 19 October, 2000:
- Lecture 9, on Genetic
Mobile Elements, has now been updated.
Thursday, 12 October, 2000:
- Midterm 1 will be next Tuesday,
17 October, 2000, beginning at 7 p.m. (unlimited time)
- The exam will be held in Centre 113 and Centre 115
- Students with last names beginning with A through M,
please go to Centre 115
- Students with last names beginning with N through Z,
please go to Centre 113
- The Exam will cover material covered in Lecture up through
Friday, 13 October, 2000
- Journal Articles 1 and 2 will also be covered on this Midterm
- No calculators will be permitted
- Smith will have extended Office Hours before the Midterm
1:
- Monday afternoon, 1 pm - 4 pm; Tuesday all day, 9 am -
4 pm
- Review Session: The TAs will have a question/answer
(non-lecture) Review Session as follows:
- Sunday 15 October, 5 - 7 pm, 1103 Muir Biology Building.
- Lecture 8, on Eukaryotic Genome
Anatomy, is now available
Saturday, 7 October, 2000:
- Lecture 7, on Prokaryotic
Genome Anatomy, is now available
- The beginnings of Lecture
8, on Eukaryotic Genome Anatomy, is available.
- The beginnings of Lecture
9, on Genetic Mobile Elements, is available.
- Words have been added to the Lectures
Web page, to clarify Topics covered in given Lectures
Friday, 6 October, 2000:
- NO Lecture on Monday 9 October !!! ... Do readings for
Lecture 6
Smith will be unexpectedly out of town, due to death in family
...
- Lecture 6, on Functional Genomics,
is now available
Thursday, 5 October, 2000:
- Some additional information on RFLPs and Pedigrees has been
added to Lecture 4, including links
to sites at NCBI and two RFLP Examples,
one with a Pedigree Analysis
Tuesday, 3 October, 2000:
- The location for Office Hrs for TA Emily Barria have been
corrected in Sections/OffHrs, to:
University Center 303, Room 204 (UCtr303, Rm 204)
- Lecture 5, on Genome Sequencing,
is now available
Friday, 29 September, 2000:
- Lecture 4,
on Genetic aspects of Genome Mapping, is now available
- The beginnings of Lecture 5,
on Genome Sequencing, is also available
- Section A06 has moved from Monday, 6:50-7:40 pm, to Wed,
11:15-12:05, after class!
This will hopefully be more attractive to students ...
Section A06: 11:15 - 12:05, York 2050B, TA: Matt Brown
- Matt Brown then has a new Office Hr: Office Hr for Matt
Brown - Mon 11:15-12:05, HSS 1306
Wednesday, 27 September, 2000:
- Lecture 3, on Cloning and High
Resolution Physical Mapping of Genomes, is now posted
- The BIMM 100 Course Materials booklet is now available at
Soft Reserves for $17.80
- There will be NO meeting of the Journal Discussion Section
this week; J. Article 1 is next week
Sunday, 24 September, 2000:
- The first two lectures are posted
... both may be updated a bit further
Wednesday, 20 September, 2000:
- These Web pages are currently being updated for Fall, 2000.
- Discussion Sections and Office Hrs will begin Monday,
25 September, 2000
| BIMM100 | Syllabus
| Sections / Off Hrs | Grading
Policy | DNASYSTEM
|
| Lectures | Journal
Articles | Study Qs | Lab
Techniques | Exams |
If you have problems or comments, send email to Doug
Smith
