THANKS, AND GOOD LUCK TOMORROW!

Dear T53 and T59 students

Thank you all for a good term. Working with you has been a pleasure; you are the most dynamic, enthusiastic, and fun BIOL335 groups that I've ever seen!

Good luck tomorrow and on all your other exams

Cheers

Pam

Q&As

Please check the link to our answers to practice questions regularly...I am posting Q&As that I got by email.

My email and other info

If you'd prefer to email me rather than posting a comment:

kalas[at]zoology.ubc.ca

Please note that I'll share your questions (and their answers) with the rest of the class (anonymously). They will be posted on the "our answers to practice questions..." site (see link on the right).

Extra tutorials:

Thursday, 9-11 am room 5458 in biosciences from 2449 go 2 floors up, down the corridor, 5th or 6th door on your left).

Friday 9-11 am, room 5458 (see directions above)

QUESTIONS ABOUT DR GRIGLIATTI'S SECTION

Please post here your questions regarding Tom G.'s section.

The least you need to know:

- eukaryotic genes: their elements and how they are regulated (think about everything that needs to happen in order for a eukaryotic gene to be transcribed in a given cell)

- the conept of "reporter gene" and how to use a reporter gene to test the activity of a cis-regulatory element (or to define it)

- how to clone a gene based on positional information

- how to clone a gene based on sequence homology

- when and how to use a Southern blot, a northern blot, chromosome walking, RT-PCR, footprint analysis (and how to interpret results)

- how to sequence an entire genome (steps involved)

- how to assemble a contig using molecular markers

- what a microarray is

- transposable elements: generalities, as well as P element's hybrid dysgenesis (in general) and how to use P elements to add a piece of DNA to a fly's genome, and how to exploit them to clone a gene

- transposable elements in a cross (like the question we did with corn and the Ac and Ds elements)

- types of transposable elements (very general-class I and class II)

Happy studying! 

 

QUESTIONS ABOUT DR. HAUGHN SECTION

Please post here all your questions about the last section of the course (cell cycle, cancer and development).

The least you need to be able to explain to yourself:

- how do you go from one cell to many cells that look different, act differently and work together in a coordinated way;

- the connection between gene expression, regulation of gene expression, differentiation and development;

- a few examples of types of proteins (gene products) that are involved in development (e.g. TF, signalling proteins, etc)

- a few examples of how the action of a gene, or that of a protein, can be regulated (transcriptional level, translational level, post-translational....)

- how you can get a cell to grow out of control (what "things gone wrong" may cause this)

- what type of mutations can affect cell cycle

- how to show that DNA element X( e.g. a module of an enhancer) is necessary and sufficient to confer a particular spatio-temporal expression pattern to your gene of interest;

Tutorials/reviews next week (april 14-18)

According to in-class (Wed.) voting, and to the few messages I got, we'll have two tutorial sessions next week:

Thursday (17th) 9-11, room TBA

Friday (18th) 9-11, room TBA

If you are able to let me know in advance what you would like to go through, please post your requests here (it will help with the choice of material to cover in the sessions).

Next week there will also be extended office hours on Tue, Wed, Thu, Fri (TAs there from 9 to 3 or 4pm every day).

On Friday (the 11th) I will post my email adress here for those who find that it's an easier way to communicate than  the blog (Q&As, with identification details removed, will also be posted here).

Happy studying!

MISCELLANEOUS

Check the course website...there may be a few extra practice problems posted.

This week, the Mon. tutorial got all the cell cycle stuff done and got started a little bit on development. The Wed tutorial will work on development as well as on clarifying possible "problems".

Next week, the Mon. tutorial will work on development (we'll get that all done); the Wed. tutorial will finish development and have some Q&A time. Monday people are welcome to join the Wed. Q&A time, and Wed people who want some extra time on development are welcome to join the Monday group.

Check the questions and answers to practice questions page regularly now...practice questions and (later) answers will come up regularly.

The week after the end of classes (14-18 of April) we will have 2 extra sessions (one for the Mon. and one for the Wed. group, but everyone is welcome to come to either or both).

POSSIBLE FORMATS ARE:

1) REVIEW SESSION

2) TUTORIAL WITH EXTRA PROBLEMS SETS

3) INFORMAL Q&A SESSION

4) OTHER (PLEASE SPECIFY)

Please choose which one you would prefer....so far we have 8 votes for 2) and 5 votes for 1) (plus one undecided)

POSSIBLE TIMES ARE

a) Monday am

b) Monday pm

c) Tue am

d) Tue pm

e) Wed am

f) Wed pm

g) Thu (finish before 11.30am)

h) Fri am

i) fri pm

So far Thu am, the 17th of April, has 7 votes and Fri am has 3 votes; Fri pm has 2 votes.

Cell cycle stuff-please post your questions on cell cycle here!

The comments and answers regarding the assigned questions for this week (available on the BIOL335 website) will be posted here on Sunday.

Have a good weekend!

HAPPY EASTER...

Hello 335 people,

as it was brought to my attention, lately it's been very quiet in this virtual space. It would be great if you could let me know what kind of materials you'd like to find posted here. Are summaries helpful at all? Lists of "study questions" (or, "the least you need to know")? We are a bit limited with practice questions...

Are there questions about techniques? 

In the meantime, I have added a few comments, notes and summaries based on previous years' requests. 

You are encouraged to post your comments, questions and requests...

Happy long weekend

Pam

About chromosome walking (seemed to be problematic in the past-please don't feel insulted if this stuff is obvious to you)

Another practice question

A practice question

Transposons-if you have any questions on transposons, post them here!

You should be able to explain:

- what a transposable element is

- what are the "parts" of a transposable element

- what types of transposable element do we know?

- what is an autonomous transposon?

- what is a non-autonomous transposon?

- how we can use P elements to insert a transgene into a fly (i.e. make a transgenic line)

- how we can use a P element to clone a gene in Drosophila based on its phenotype

- what are the "clues" that suggest that a mutation is due to a transposable element.

If anything is unclear, please ask...

Cheers

Pam 

Sequencing of an entire genome

For the genomics chapter.....

....check out the "our answers to practice questions,..." link: I am posting practice genomics questions there. I'll also include questions from the old textbook.

Please let me know ASAP if you have any questions regarding this chapter (13)! 

And remember to try asking Tom G. questions in lecture....

Cheers

Pam

PS: your eukaryotic genes are available for viewing in this gallery... authors please identify yourselves and, if you wish, choose a title for your work!

ABOUT Q24, CH11

Sung Soo kindly compiled and provided a summary of what we discussed regarding question 24 in chapter 11 (the one with the RNA blot and the 4 clones).

Here it is!

Last week before reading break-summary

The topics were eukaryotic gene regulation, a bit of epigenetic inheritance and a couple of questions from the book. Here is a summary on what we said about gene regulation. Let me know if you have any quesitons or comments!

I am also preparing a "eukaryotic genes" gallery with all your drawings...I'll let you know where to find it.

Summaries about what we said regarding the book's questions will be posted soon. If you'd like a quick (one paragraph or so) summary on epigenetic inheritance, please let me know!

Cheers

Pam

T59-what we did last monday

Last Monday (after the midterm) we basically went over problem set 4. You can find a summary of what was said under the "our answers to problem sets..." link ( or by clicking here).

If you have any questions regarding problem set 4, please post them under this section.

Thanks!

Pam

MIDTERM

Please post here all your thoughts, comments, ideas (positive and negative), and questions about the midterm.

Tutorials for the week of Feb 11-15

Hi T53/51 and T59 students!

Your next tutorials will deal mainly with eukaryotic genes and how they can be regulated. We will go through everything you need to know  about this (all the elements of the system, how they interact and how we can study them).

Please go over your notes....we'll go through all the concepts and information needed to answer the assigned questions (although we won't necessarily do all the questions as they are in the book.).

For those who have the 8th edition of the book (green cover), the eukaryotic gene regulation stuff is  in the second part of chapter 10, and the assigned questions correspond to your chapter 10 # 13, 14, 29, 23 and 30. 

Please let me know ASAP if you have any particular requests (conecpts or questions to go over, etc).

Have a good weekend

Pam

TUTORIAL WEDNESDAY

Dear T59 students,

due to the threat received for tomorrow, to the cancellation of many biology classes (which probably means that several of you may decide to stay home-and rightly so), and to the possible confusion that may result from all of this, tomorrow (WEDNESDAY)'s tutorial will be cancelled and re-scheduled to a date that is convenient for everyone.

I am very sorry about this disruption, but I believe that in a situation like this one everyone should feel free to decide to stay away from campus without any consequences (such as missing out on information, etc, given in a tutorial). 

The topic of the week is problem set 4, and I am sure we'll find a time to go over it together. In any case, I will post explanations, hints and, eventually, answers by this weekend.

See you all next week, and be safe!

Pam

This week's tutorials

I hope everyone did well on the midterm...

... and that everybody remembers that this week's tutorials will take place as scheduled.

T51/53 will be in Hebb12 on Monday and T59 in FSC 1613 on Wednesday.

Please bring your problem set 4!

Questions on ORFs and cloning

Please post here alll your questions and requests regarding ORFs, cloning and related material.

Questions on restriction mapping

Please post here all your questions and comments on restriction mapping, problem sets 1 and 3, chapter 20, Southern blots and techniques in general.

Questions on lac operon and bacterial gene regulation

Please post here all your questions and requests regarding lac operon, problem set 2, chapter 10, and other topics relating to regulation of gene expression.

Last year's students suggestions on restriction mapping...and Pam's answers to some questions

Answers to problems set 3 and some extra practice problems will be posted during the day (Thursday). I'll update you on the availability of the paper-based extra problems.

Practice question (more to come-look also at the links)

WEEK 3 SUMMARIES

You can find them here under "answers to questions that came up..." 

A reminder: this week (Jan 28-Feb1) will be your last week before the midterm. Make sure you go through your notes, the instructor's note, all problem sets and flag anything that's unclear! Take advantage of office hours, tutorials, etc! I am away next weekend until Sunday afternoon, so I won't be able to answer your questions by email or through the blog-don't wait until then!

T53-Monday

T53 will meet in Hebb 12!

(2-3.50 pm)

Please bring your problem set 3 (by the way, it comes right out of the 8th edition of the book, chapter 11). 

Thanks,

Pam

For those who have the 8th edition of the textbook (the green one)

Here are the "equivalencies":

9th edition (white) chapter 20 is chapter 11 in the 8th edition.

Questions 4,5,16 and 17 in the 9th edition are questions 4,6,29 and 30 in the 8th edition.

PRACTICE QUESTIONS AND ANSWERS

Here are two extra practice questions for this week. 

You are also encouraged to make up your own lac operon practice questions by listing as many genotypic combinations as you can and trying to figure out whether you will produce B-Gal and/or permease in the absence and in the presence of inducer and/or glucose!

Our answers to problem set 2, and a short summary of this week's sessions will be up by tomorrow (the link is under the BIOL335 links on the righ-hand side).

Let me know if there's something specific you'd like me to post here!

Pam

Wednesday tutorial-T59

Hi T59-ers!

Please bring your problems set 2 to tomorrow's tutorial...

We'll work on the lac operon and on problem set 2.

If you have already done all the problems, be prepared to explain your rationale because your classmates will be curious!

I have compiled a list with your expectations and will bring it to the session.

Cheers,

Pam

SUMMARY

For the Wednesday crowd:

all the lac operon stuff will be in week 3's summary.

For everyone:

feel free to comment, ask, rectify, etc, on this summary!

A friendly note: although I collated and edited this summary, its content represents the work of everyone in T53 and T59. It is not intended to be sold or distributed for profit without the consent of all contributors.

Monday tutorial-T53

Hi T53 people,

1) I will post a quick summary of "what you need to remember/understand" from week 2 (this week)-it will be up for sure by Sunday evening.

2) Please bring to Monday's tutorial a copy of Dr. Beatty's problem set 2. We'll work on it and we'll systematically construct (together) a list of tricks and rules to use to interpret and solve operon kinds of questions.

The main concepts of Monday's tutorial (subject to change):

- cis-acting vs. trans acting and what we can use this for

- positive vs. negative regulation, and how we can tell which one is at work

- some details and oddities of the lac operon

- some very successful ways to lose marks on an operon exam question!

Cheers

Pam

A LAC OPERON QUESTION

You'll find more practice questions on bacterial gene regulation under "Pam's lac stuff". Answers will be posted under the "our answers to..." link.

WELCOME TO OUR VERY OWN 335 VIRTUAL SPACE!

Greetings, BIOL335 T53 and T59 students!

The purpose of this blog is to keep you in touch with your classmates and with your TA during the week. If you get stuck on a problem, have a pressing question, would like to know more about a certain topic, or simply have a request for the next tutorial session (e.g. "Can we go over how to clone a gene based on sequence homology?"), you can easily leave a comment and within 24 hours you'll get a response/answer.

Announcements, "practice questions", summaries, and last minute changes regarding our tutorials will also be posted here.

Finally, this is a perfect place to give your TA some feedback (comments are completely anonymous), to share ideas, tricks, fears and concerns with your classmates, to complain about how hard the midterm was and, last but not least, to try and answer some of the questions that other people have posted.

PLEASE NOTE: 

this blog DOES NOT, by any means, replace the course website 

(which you can find under the BIOL335 links list).

ENJOY YOUR COURSE!

Pam

One more thing....I WILL BE IN THE HELP ROOM (2519) MON+WED 4-5PM.