Mitosis notes

Jellies (and Squids if you want them)- There is a new PDF of the mitosis slides with notes added, since I was out for the lecture yesterday.  Review them over the weekend and I will clear up any questions on Monday.

For everyone- continue working on your osmosis lab final.  Email me if you have questions (I won't be checking comments on the document until I grade the finals).

Squids- Finish up the stem cell activity if you didn't finish it in class.

In class work Wednesday Dec 17

Good morning Jellies,

I am out sick today. In class you should do your best to fill in the Mitosis notes found in the Unit 2D folder. You can use the reading (mitosis reading, 2D folder) or other online sources to help you. The most important part will be recognizing the phases of mitosis- the reading has some nice pictures. We will do a lab tomorrow and then fill in any gaps in your notes next class. Be sure to do the activity on the last slide (only takes about five minutes). 

Mitosis homework

Homework after the mitosis (PMAT) lecture: finish the mitosis reading on the stages of mitosis.  Continue to work on lab final (due Tuesday).

Monday night HW

Read pp 82-84 in the mitosis reading found in the unit 2D folder.  You should continue working on your lab final as well- those are due next Tuesday (last day before break).

Link to HHMI cell cycle page: http://www.hhmi.org/biointeractive/eukaryotic-cell-cycle-and-cancer

Misconception

As I read through your introductions I am seeing a common misconception, that the reasons ions can't get across the cell membrane is due to the charged phosphate group.  This might be a small factor, but the main barrier to ions are the hydrophilic tails.

I think the problem may be due to the way the phospholipid bilayer is drawn, like below.

From this diagram it looks like the hydrophilic portions are large and act as a barrier.  But in reality the phosphate group is pretty small compared to the hydrocarbon chains.  Below is a space-filling model (closer to the real structure).

Here you can see that that portion is fairly small.  

So, to summarize, if you are going to discuss why ions can't cross the cell membrane your primary reason should be that they can't get across the lipid portion.

Weekend HW

-Make sure you have completed the notes on Lessons 17-20 (17 and 18 we did in class.  If you are doing these on your own, note that we only did the last third or so of lesson 18).

-Answer the questions on the strawberry lab and share in your folder.  If you didn't do it in class you can do it at home- it only takes 10 minutes and everything you need you can get at the grocery store.  Use rubbing alcohol for the ethanol and an unfolded paperclip for the extraction loop.

-Read and take notes on the DNA replication reading in the 2D folder.  Pay attention to the steps of replication as well as the purposes of the three enzymes helicase, DNA polymerase and ligase.

Here is a really good animation of DNA replication (but unfortunately it doesn't work on iPads).  Don't worry about the RNA primer or about any of the enzymes besides the three we discussed in class.

**ALMOST FORGOT!!***  I am in the process of giving feedback on your osmosis labs.  Jellies are all done.  Squids, I will be done with yours by the end of the day today.  Finals are due Dec 23rd.  Remember to check the rubric in the Unit 2C folder.

Wed night HW

If you have access to a laptop or desktop, finish up your notes through the end of Lesson 19.  Then do the following:

Read the Wikipedia page on Rosalind Franklin.  Hers is a famous story in science about the failure to recognize the work of all contributing individuals as well as the sexism that was common and accepted at that time.  

Note: James Watson, one of the two scientists described in this lesson, worked as director, president and chancellor at Cold Spring Harbor Laboratory (the institution that runs the dnaftb.org site) for nearly 40 years.  This may explain why there is no hint of controversy over Franklin’s contribution in Lesson 19, although nearly all other publications at least mention this in passing.

HW after quiz

The link to the page with the animations is here.  Remember that the animations do no work on the iPad.  Additional information about the three experiments we looked at in class can be found here.

For homework, read this page which summarizes the work of Watson and Crick to elucidate the structure of DNA.  We will look at that animation (lesson 19) in class.  I highly recommend using printfriendly.com to convert the webpage into a PDF that you can bring into Notability to take notes on.

Transport Across the Cell Membrane Quiz Next Class (Mon/Tues)

Like the last quiz, you may bring in one 3x5 index card that has handwritten notes on one side. Squids- I forgot to give you cards.  You can bring in your own or just use a 3x5 piece of paper.

The quiz will cover all types of transport and include a few questions about cell organelles.  I would read over the organelle notes in the folder but I wouldn't dedicate a ton of time to organelles.  If you have the opportunity, studying together is a good way to check your understanding of the material.

The quiz is only 28 multiple choice questions.  We will start the next topic as soon as the quiz is done.  

Osmosis Lab write up

Draft of the Introduction and Results section due on Friday.  More detailed information will be in the Unit 2C folder, as well as sample papers.

Osmosis Lab

Jellies- make sure someone in your group emailed me a list of materials/equipment needed by 2:30 today (Monday).  If its not on the list, you won't have it for your lab!

HW is to come up with a list of procedures so that you know what to do when you come in tomorrow.

Active Transport

HW: read the rest of the same page (no really, this is the link, sorry for the bad link earlier) except for osmosis.

Here are links to the videos we watched in class today:

1. Sodium Potassium Pump
2. The nerve cell and action potential
3. Cystic Fibrosis (only first 5 min or so)

Diffusion

Finish any calculations or questions from the agar cube lab.  Turn this into your shared folder.  Next, read the Diffusion and Facilitated Diffusion sections of the following page:

http://www.uic.edu/classes/bios/bios100/lectures/diffusion.htm

You should absolutely be taking notes on these to help your understanding.  I would click on the picture (title) for each concept and label the diagram with the concepts described in the notes.

HW after quiz

Import your section's organelle notes into Notability.  Read these notes, underline and highlight as needed.  We will continue to discuss the cell and parts of the cell next class.

Quiz on Monday

Quiz on Biochem (nothing on the organelles we just started).  The vocab list will give you an idea of the topics covered.  Check your notes, the reading and the PDFs of the slides.  Format is multiple choice with one open-response on enzymes.

I'll be in around 7 or so on Monday morning if you'd like to come by with questions.

ALMOST FORGOT: Reminder that you can bring in a 3x5 notecard with handwritten notes on one side.


Have a good weekend!

Cell Structure: Organelles

Wednesday night (due Thurs/Friday): Read Ch 7, lessons 1 and 2 from the textbook.  Fill in the notes found in the Unit 2B: Cell Structure folder.  The notes on each organelle can be brief- a few words or phrases.  We will look at them in more detail in class.

Updates

A few things...for class on Wednesday everyone should be preparing a brief summary of the catalase lab results to present to class.  You should state

• your hypothesis
• your procedure, including variables, constants, controls
• your results
• any conclusions you can draw from results regarding enzyme activity

We will wrap up with enzymes on Wednesday.  I mis-identified the reading from the textbook...it is NOT Ch4, but Lesson 4 in Chapter 2 (enzymes).  Sorry about that.

Finally, there was a request to move the biochem quiz to next week so as not to conflict with the upcoming History test. OK.  Quiz on Monday for both sections, so I'm expecting 100% all around, mm-kay?

Almost forgot- you can bring in a 3x5 index card with hand-written notes on ONE side for the quiz.  No excuses now.

Post-Catalase Lab

If you did the full catalase lab today (Squids Friday, Jellies Monday) you should review your data and decide if it supports or contradicts your hypothesis.  You and your lab partners should be prepared to briefly present your data to the rest of the class (so that everyone can hear how the different factors tested affected enzyme function).  If you didn't read the section in the textbook yet you can do that too (see previous post).

There will be a quiz on Biochem at the end of next week (November 13th or 14th).

Enzymes

HW tonight will be to read from the textbook.  The link to download the textbook is in a Google Drive word document called "Untitled Document."  First make sure you have iBooks on your iPad, then click on the link to download the text.  It could take several minutes.

Once you have the book, read Ch 2 Lesson 4 on Enzymes (its not long) on enzymes.  Pay attention to how the shape of an enzyme is essential to its function.  Recall how the 3D shape of an enzyme is determined.

Updated- the reading above is important to do- definitely before the biochem quiz (end of next week).  But your primary focus tonight should be lab prep.  You should have

• a list of all the materials you need
• list of procedures
• a data table or some other place to record results
• and of course, a hypothesis (what will you vary?  what results do you predict?  WHY is the variable affecting the enzyme function?)

Don't forget- today (Thursday) is the LAST DAY I am checking your folders for Q1 homework.  If its not in today its a zero forever!

Link to enzyme video.  There are many others as well.

Protein Folding Lab

HW for tonight- finish the questions to go with the Protein Folding Lab.  When you are done, send them to your Drive folder and create some sub-folders: Q1, Q2.

Also, LAST CALL for Q1 work.  Some of you didn't turn in the Properties of Water or Dehydration Synthesis.

Nucleic Acids

Monday night: Read pp 80-81 on nucleic acids, AND 70-76 on protein structure.

Lipids

HW for Thurs/Friday:  Read and take notes on the section on lipids: pp 67-70.  Pay attention to the way that the chemical structure of lipids determines the characteristics of these molecules.

Carbs

HW for Wednesday night: read and notes Carbohydrates: pp 59- 66.

(note: the text calls dehydration synthesis "condensation."  You can think of it as the monomers condensing into a polymer.)

You should focus on vocab words, as well as details to go in the chart we worked on in class.  Pay attention to how the shape of the polysaccharides affects the role that the molecule fulfills for the cell.  As you read fill in any notes in the outline from class that you didn't get to. 

Dehydration Synthesis and Hydrolysis

HW Monday night/Tuesday night is to finish the dehydration synthesis activity.  Yes, you can Google.  That means you can research info to help you answer the questions, learn more about dehydration synthesis, hydrolysis, etc.

For example, here's a handy animation showing dehydration synthesis and hydrolysis.

Biochem reading

There is a PDF in the Unit 2A folder called "Organic Molecules Reading."  For Monday, read and take notes on pp. 54-57, starting with the summary about water on p 54.  Then focus on the characteristics of carbon and the structure of the functional groups on page 57.

Wrapping up Unit 1

Tonight look over the document in the Unit 1 folder called "The Results section."  There is additional information here on what I am looking for in the final version of your Bird Beak results.  Final due Friday.

Make sure you (or your partner) turned in the cladogram picture from the in-class activity and the Earthviewer document.  Everyone should also have turned in "Qs to go with Origins How Life Began."

The End of Q1 is next Friday.  All work needs to be in by then.

Happy studying!

End of Evolution Unit

Final assignment in Evolution is to watch portions of the Origins: How life began video (link here). Answer the questions on the document in the shared folder.

Also in the folder there is a list of topics and resources called "Evolution Study Guide."  You should at least look this over the final day before the test (Squids Friday, Jellies Monday) and come prepared with questions.

Don't forgot to make sure that you or your partner turned in the "Earthviewer" Qs.

Test on Tuesday 10/21.  Final of Results section due 10/24.  We'll talk more about the results section before the final is due.

Just kidding...evolution never ends!

Macroevolution

For HW, start reading here, and read to the end (where it says "You have now reached the end of Evolution 101...").

Make sure your Results draft is in.  Final due Friday 10/24.

Test on Evolution on Tuesday 10/21.

Cladogram activities

What did T. rex taste like?  Go to student start, then choose folder 3.  Complete folders 3 and 4.  This activity works on the iPad.

Build a cladogram.  Start by filling out the data table.  This one does NOT work on the iPad.  Complete using a laptop in class or at a home computer.  Use your iPad to take a picture of the cladogram you drew and send this to your shared folder.

Homework: start here, read the next four pages (much of this is review of what we did in class).  When you get to the five examples of using the trees (whale, cichlid etc) you can scan/read briefly.

Speciation reading

For HW tonight read and take notes on the following:  start here, and read up through Cospeciation. Stop at Macroevolution.

Don't forget to work on your Results section draft as well.

The Results Section

Draft of a Results section due on Friday.  Check the notes in the shared folder.

Here's what you should include for EACH of the three parts that we did (Natural Selection on Day 1, Mutation and Gene Flow on Day 2):

• A data table
• A graph or chart the BEST shows the changes in allele frequency that occurred over the generations
• A short paragraph describing the results in words along with any trends that occurred

You should also include a data table and short paragraph about the seeds on the island (from Day 1), as well as the Chi-squared analysis for Natural Selection (you can either type it out or write it in Notability, then import it as a PDF or take a screen shot and bring it in as a picture).

When you are done everything should be on ONE document.  You'll have to decide where it is easiest to assemble it all (Notability, Drive or some other program).  Neatness and organization of your sections will contribute to the grade for the final (draft due Friday).

The snail paper and motorcycle paper are available in the shared folder if you want to take a look at real results sections.

Other processes in evolution reading

For HW tonight (Squids Tuesday night, Jellies Wed night) please read and take note on the following pages from the Berkeley Understand Evolution pages.  Most of this is similar to what we talked about in class today so you shouldn't need to be taking huge long extensive notes- just make sure you understand the processes we talked about today (sexual selection, drift, etc.).

You can use Print Friendly.com to turn these pages into a PDF, but you would have to do that for each page which could be time consuming.  You could also try copying all the text into a word doc, or take screen shots of each page.

Here is the link: Begin here.  Read up to Coevolution (also see menu on the left of the page).  Most pages are short on text and include diagrams.  Also please note that on the Genetic Drift page there is a link on the right that explains about bottleneck/founder effect.  Also here: Bottleneck and Founder effects.

Artificial selection gone too far...

Sexual Selection- video and Qs...

...now in the Unit 1 folder.  Complete and turn into your folder for credit.

Homework Credit

To clear up the confusion around turning in, homework credit etc.

1.  I decided I don't really like that turn-in form.  This is the first time I'm teaching completely electronically so some stuff isn't working out the way I anticipated.  If you put your work in the folder (the one with your name and section) that is fine.


2.  I hadn't planned on checking and giving credit to for the Beak of the Finch questions but I can do that.  If you finished Qs1 you can turn them into the folder.  Qs2, which are due on Monday, can also be turned in.  I won't be commenting/correcting them since we are discussing them in class.  But I'll give you hw credit.


3.  I haven't forgotten about your Yeast Labs.  Any day now.

Beak of the Finch Pt 2

The second selection of Beak of the Finch is in the folder, along with the questions.  You should jot down notes to answer the questions but they don't need to be paragraphs or even sentences.  Just be ready for discussion.

I'm posting this now so it is available but it isn't due until Monday.

Reading- The Beak of the Finch

The Beak of the Finch recounts the story of one of the first studies to actually show evolution happening as researchers watched.  The husband and wife team of Peter and Rosemary Grant studied the finches of the Galapagos Islands for decades, sometimes witnessing evolution (that is, change in the relative frequency of various genes) occur from one season to the next.

For homework read the posted selection from the book.  Then answer the questions and turn them into your folder.

Weekend Homework

Up next we'll be taking an in-depth look at Evolution.  For Monday please watch up to 22:30 of this video (From the 2001 PBS Series Evolution, Episode 4: The Arms Race).

You should pay attention to the two stories presented in this section: the arms race between the snakes and the newts, and the evolution of antibiotic-resistant TB bacteria.

Questions to think about:  How did the newts evolve such a potent poison?  How did the snakes evolve resistance to this poison?  Why do bacteria evolve so rapidly compared to people (as in, how come they became resistant to medicine and we didn't become resistant to them)?  Why would certain individuals in each of these populations survive or perish?

Take some notes on these two stories and jot down any ideas or answers you have regarding these questions so we can discuss next class.

Have a good weekend!

ZOMG!QUIZ TOMORROW WHAT SHOULD I STUDY I SHOULD PULL AN ALL-NIGHTER!?!?!

No.  It's going to be fine.

If you have been paying attention in class (taking notes, asking questions if you are confused), and reading for understanding (NOT reading for memorization), you will be fine.  You should know and understand everything we talked about in class.  PDFs of the notes are all in the folder.  You should understand the readings- the big ideas of the readings, that is.  I could include a paragraph from the reading on archaea and ask you to explain why it supports classifying these organisms in their own domain.  You can all do that.

If you are still uncertain study with others in the class.  Email me if you must.  If it all truly falls apart we'll talk about a retake.  The point of this quiz (and all future tests and quizzes) is to see what you know and can do.  Just a quiz, people.

The Story of Cold Fusion

Here is the link to the full story: Cold fusion: A case study

More Classification

Read and take notes on the following pages regarding the three Domains and four Eukarya Kingdoms.

From Animal Diversity Web on the process of taxonomy

From the Encyclopedia of Life: Archea

Also from EoL: Bacteria, Protists, Fungi, Plants and Animals.  Be aware that there are several characteristics that MOST, but not all animals have.

Reminder- Quiz on Friday covering Characteristics of Life, Classification and Scientific Method

Scandal- reproduction in the lab!!!

Here's a photo I took today from some yeast that's been sitting around in water and sugar for a few days:

Those are some lively live cells.  Have a good weekend, everyone!

How we classify today

For Homework read the following pages from the Understanding Evolution site by UC Berkeley. You should already know why it is essential for a classification system to take evolutionary history into account.  These pages will teach you more about the methods used to elucidate the evolutionary relationships between various living things.

Begin here, read this page and the next two (to the bottom of the page with the orchids and the cats). You might want to turns these pages into a PDF (using Printfriendly.com) and bring into Notability to mark up your reading and save your notes.

As you read, focus on the ways that phylogenetic trees recount the history of evolution, as well as the reasons that the Linnean system is not as useful now.

Characteristics of Life

Two days worth of HW here:

For HW the night after you do the lab, you should write-up a brief summary of the procedure (what did you do and why), the results, and a discussion of your results.  The discussion should include any mentions of errors or issues with the lab/procedures.This does NOT need to be a formal write-up; it's more like notes you would keep in a lab notebook, a narrative (ie, ok to use first person).

For HW the night after the lecture, you should write an introduction of background knowledge about the characteristics of life.

Each person needs to complete this in their own words (not one per group).  Save to your shared folder and turn in using the form.  This doesn't need to be turned in until you've done both days (the lab day and the lecture day), so Squids due Friday, Jellies due Monday.

Let's do some science!!

Time to start putting some skills into practice.  We will be examining the characteristics of life in the lab using yeast.  Everyone knows that yeast is alive, even though it looks completely inert when you take it out of the package.

Your assignment is to come up with an experiment to demonstrate that yeast possesses the characteristics of life.  Choose just one characteristic to focus on.  This experiment needs to be set up, performed and completed (with clean up) in one class period.  Think about:

• variables and constants
• control and experimental groups
• quantitative vs qualitative evidence
• equipment and materials needed (limited to whatever is available in the lab)
• what information needs to be recorded for your (brief) write-up

Before leaving class choose 2-3 other people to work with.  For HW, write up a brief procedure addressing the points above (this can be done collaboratively).

Science Literacy

There are lots of pieces to Literacy in Science.  Some of it is just regular reading and writing (do you understand what the text is about?) but the more sophisticated part is evaluation.  How valid is the claim or results that the author is describing?  What personal or cultural biases might be influencing results or interpretation?  Remember, "science is meant to be objective, but it is practiced by humans, who are not objective."

Choose a recent (within last year) article describing a study within Biology (health and medicine, climate, environment, biodiversity, cells, etc.).  You can choose an article directly from a journal, such as Science or Nature (if you can access the whole thing), or an article from the science section of a popular publication, such as the New York Times.


Your assignment:

1. Read the article.  (Click here for instructions on turning any article into a PDF using Printfriendly.com, in case you want to mark it up in Notability).  Read it for comprehension and to evaluate the validity of the results.

2.  Write a 2-3 paragraph summary of the article.  Briefly describe the methodology and results.  Discuss any factors that might affect the validity of the results.

3.  Drag your document into the Drive folder you shared with me (a few of you haven't made your folder yet!).  Then, copy the link and go here to turn it in.  Save this link for future use.

**Almost forgot- please return your signed safety contract as well**

Due by the start of the next class meeting (Monday the 8th for both sections).

Here, this should help you get started (from compoundchem.com)

Shared folders on Drive

Day One Tasks (2 parts)

1. Look in your Drive for a shared folder from me (Jellies or Squids).  Find the Unit 0 folder, open and read the Policies and Procedures.  Please contact me with any questions.

2. Create a folder with the following title: <Lastname> <firstname> <section>.  Share this folder with me.  This is where you will turn in completed work.  Your classmates will not have access to your assignment folder.

HW: Download and complete the Safety PDQ from the Unit 0 folder.  You do NOT need to share your completed HW back to me.  I will check it in class.

Jellies- this HW is due Thursday; Squids on Friday.

For today only (and for parents and guardians to see) here is the Policies and Procedures Info

and Syllabus

Getting Started

Welcome everyone!  Hope you had a great summer.  The first few days are just going to be about getting organized, especially with all things technology.

1. Please open this form and save it to your iPad's home screen:
Darlington Sign In Sign Out Form
You will use this form to sign in/out for bathroom breaks, visit another teacher, arriving late, etc.

2.  Complete the student information survey for homework.  Please answer questions thoroughly.  Your responses will help me to get an idea of how you learn, and what I can do to help you.