The fluid-mosaic model

Today, we modeled the structure of the molecular structure of the cell membrane and discussed how it's unique "fluid mosaic" structure allows for a diversity of functions - semipermeability, protection, cell transport, cell identification, and others.  All in all, it's one of the most functional and varied parts of the cell.

Homework
Your homework is to explore an online demo / tutorial of the cell membrane.  The tutorial is awesome and very interactive - you can click around and see how the cell membrane moves, what the components do, and how it is structured.  It is partially a review of what we talked about in class, however there's a lot of new information to, so read and explore carefully (you could easily spend a half an hour here and not exhaust this resource).

The tutorial can be found here: Cell Membrane Tutorial

Using the online tutorial as a text, you should be able to complete assessment statements 2.4.1-2.4.3 in your notebook.  Please note that the tutorial has more information and detail than you need for the assessment statements - focus in only on the information required for these assessment statements, rather than get bogged down in every petty detail.  Details are important, yes, but fortunately the IB gives you an idea of which details are important and which are not.

Diffusion

Hi all,

Today we examined the diffusion of dye in model cells in beaker environments.  We applied the definition of diffusion - the passive movement of molecules from areas of high concentration to areas of low concentration in order to reach equilibrium - to our model cells in their beaker homes.  Additionally, R4 devised a method to determine the rate of temperature on diffusion, and discovered that heat increases the rate of the diffusion of dye.  This makes sense, since diffusion is essentially the movement of molecules, and heat makes molecules move faster.

Here are some helpful animations about diffusion that reveal it's molecular nature.  The second one we will use in class tomorrow:

How Diffusion Works
Perfume Diffusion Simulator

Check these out! They are very helpful at visualizing the molecular level.

Homework
Tomorrow, we are going to examine the structure of the cell membrane to see how it manages to be both a barrier and a window, selectively letting some molecules in and keeping others out.  In preparation for the activity tomorrow, please pre-read pages 84-86 in your textbook about the cell membrane.

Thanks,
Mr. Hill

Classifying cells and gazing into the past

[UPDATE: Thanks to Jennifer for the pictures of our giant tape venn diagram.  The picture quality is pretty good - you can see all the parts (and use this for your reference!)  Also check out the photo of the middle of the venn diagram - that is, the "first cell" we talked about.]

On Friday, we used a giant venn diagram to describe the characteristics of three types of cells: prokaryotes, eukaryotic animal cells, and eukaryotic plant cells.  We noted that though there are many differences, cells all share a few basic features: a membrane, wrapped around some squishy stuff called cytoplasm, which has some instructions (DNA) and some machinery to carry out the instructions (ribosomes).  We can hypothesize that the first cell had these basic features.  There's been a lot of curiosity about just how this first cell could have popped into being.  Fear not!  We'll be revisiting this question as we study the nature of the cell membrane, one of the ancestral components of the cell, throughout this coming week.

We also discussed the role of lysosomes in digestion for animal cells.  Here is a very useful animation of lysosomal function: Lysosomes: The "little stomachs" of the cell

Homework
You should continue to work on your assessment statements.  I am considering moving the unit test up one day to October 8th, so don't fall asleep at the wheel with your assessment statements!  It's coming sooner than you know.

Also, both classes should prepare for a quiz on 2.2 and 2.3 on the Tuesday we return.

Enjoy your day off!
-Mr. Hill

Plants: More like you than you know

Today, we looked at Elodea, a freshwater pond plant, under the microscope to observe some of its large organelles - the cell wall, chloroplasts, and central water vacuole.  Although on the surface plants look quite different from us, when you get down to it, we really have a lot in common.  After all, we're both Eukaryotes (we have nuclei), and our cells share many of the same organelles - mitochondria, endoplasmic reticuli, golgi apparati, plasma membranes, ribosomes - plants have them all too.


Here's a light micrograph of Elodea (another nice thing about light microscopy is that it produces color images):

And here's a nifty electron micrograph of a plant cell, with less color but much more detail:

Homework
R4 should complete their annotated drawings of Elodea to turn in tomorrow.  R6 should complete the homework on Prokaryotes posted on Monday, September 21st.


Please note that there will be a quiz on cell parts (2.2 and 2.3) on the Tuesday we get back from our long weekend.


Best,
Mr. Hill

Our cells "inner skin"

Today, we learned about the endomembrane system, a network of "inner skins" that organize the cell and manage the production and secretion of sensitive chemical substances such as hormones, neurotransmitters, enzymes, and other proteins.

For review, here is the helpful animation I showed in class: Tutorial of the Endomembrane System.

[UPDATE 10/1: I have added the Lecture notes.  They can be found here: Endomembrane System Lecture]

Homework
Continue to work on your assessment statements, particularly 2.4.7, which is largely based on today's lecture.  You may refer to textbook pages 70-73 for more information.

All pictures are from real electron microscopy of cells (mostly liver cells).  It might be advantageous to follow the lead set by James in R4 by printing the micrographs and pasting them directly into your notebook.  In your class journal, identify the structures and state evidence for why you think it is that structure.  In other words, be thoughtful: how do you know?

1. What structure is shown below?  How do you know?

2. What structure is shown below?  How do you know?

3.  Five structures are labeled in the diagram below.  Identify them and state evidence. [9/24: Note - I updated this with the labeled micrograph in order to alleviate some of the confusion we had in class in annotating the diagram.  The questionable organelle IV was in fact the rER.]

Eukaryotic cells

Today, the classes looked at Eukaryotic cells - that is, cells that have their DNA contained inside of a membrane, the nucleus.  Eukaryote come from the Greek roots "Eu-", meaning "good", and "kary-", meaning kernel: literally translating as "good kernel."  That's a little egocentrism on the part of biologists.  Originally, we thought Eukaryotic cells were "good" because they were the type of cells we had - cells with nuclei.  Prokaryotic cells - or cells that came "before the kernel"- had no nucleus and therefore must be bad.

R4 drew, labeled, and annotated a cheek cell, while R6 drew, label, and annotated a Elodea cell.  That gives us two types of Eukaryotic cells, the animal cell and the plant cell.  There are many other types of Eukaryotes, including single-celled Eukaryotes like the Paramecium.  However, in general we'll be discussing plant and animal cells as our main examples of Eukaryotes.

Homework
Your homework is to finish any drawings you owe me, and also to pre-read pages 70-73 in your textbook about the endomembrane system.  Remember, pre-read means scan over the headings, diagrams, and captions.

-Mr. Hill

Prokaryotes are EVERYWHERE

Did you know that humans, on average, have about three pounds of E.coli and other bacteria living in their gut?  Considering that most bacteria are fewer than 10 micrometers in length and have a weight to match, that's a lot of bacteria!

Today, in R4, groups of students worked to debrief a textbook reading about prokaryotes and answer the question of how single-celled bacteria survive.  You should now be able to draw and label a diagram of E. coli, one of the most abundant prokaryotic species, and annotate the diagram with the functions of each of the major structures.

The textbook diagrams, however, are misleadingly clear.  In reality, the parts of E. coli aren't quite so easy to pick out.  But all the parts we discussed are there - check it out:

Homework
Your assignment is to answer the questions below about this particular prokaryote.  Use looseleaf or an index card.

1. Determine the length of this prokaryote using the scale bar.  Show your workings.
2. Identify the structures labeled I, II, III, and IV.
3. Explain how I, II, III and IV enable the prokaryote to live.

This is due Tuesday for R4 and Friday for R6.  Remember that R4 has a short quiz tomorrow.

Surface Area, Volume, and Cells

On Friday, we used cubes as model cells to gather data about how surface area and volume change as cell size increases.  Many of you were quite sharp in observing how a cell's smaller size allows it to maximize its surface area and minimize its volume.  We generated this graph with your model cell data, where green represents volume and blue represents surface area:

Surface area is so important to a cell that they have arrived at all sorts of tricks to maximize their total surface while keeping their volume the same.  There's a good summary of how different organisms cope with the "efficiency problem" posed by SA:V ratio here: Beating the SA:V Ratio Problem.


Homework
Prepare your assessment statements based on the work we did this week.  For each assessment statement, please follow the "magistri guidelines" in order to achieve maximum credit.  For example, for 2.1.5, about calculating magnification, it is essential that you show two sample problems.  These can be taken from our classwork.  Feel free to even cut out and paste in the images from the homework handout.


Your first quiz will be on Monday for R6 and Tuesday for R4 (same as lab day).


Have an excellent weekend!
-Mr. Hill

Powers of Ten

Hi all,

For homework tonight, please watch online the short video "Powers of Ten", which can be found here: http://www.powersof10.com/index.php?mod=register_film. You need to provide your e-mail in order to view the film. If you don't want to do that, look it up on YouTube - it's there.

After you watch the video, please respond to these questions on a single side of a large index card.

1. What's the best metric unit (meters, millimeters, micrometers, etc.) to measure the following items: (a) atoms (b) a skin cell (c) bacteria cells (d) viruses (e) mitochondria (f) width of a human hair (g) a DNA molecule (h) an atom

2. Why do you think are cells so small? Is there an advantage?

This is due tomorrow. Happy watching.
-Mr. Hill

We are made of cells

Hi all,

At this point, everyone should be able to outline the three major tenets of the cell theory and discuss some of the evidence that supports the theory, as well as some arguments against it.  Some top-notch questions have been raised in the past few days, including:

1. If all cells come from pre-existing cells, where did the first one come from?
2. Is a virus isn't made of cells, can it still be considered living?
3. If we found another planet in the universe and it had some form of life that wasn't cellular, would we have to change the cell theory?  Can we know for sure that non-cellular life is out there?  How would we recognize it if we saw it?
4. How do we define life? Is there any validity to the categories of "life" and "non-life"?  Does it matter?

All good thoughts to chew on as we move forward in our discussion of cells.

Also, this is a cool picture of a nerve cell tissue that we discussed in class. 

Homework

Complete the four magnification problems on the worksheet handed in class.  This is your first shot at IB-style questions, so work methodically and carefully.  This assignment is not available electronically.

First lab

By this time, both classes have completed our first lab.  The task was to observe a cork cell under the microscope, draw it, and then determine how much larger the drawing was compared to the "real" cell.

All groups in all periods were successful at devising a way to measure the actual cell - and remarkably, many of you figured out different ways of doing it that were plausible.  The most common techniques I noticed were:

1. measuring the pointer and using a ratio 
2. measuring the image of the cell in the eyepiece and then working backwards using the magnification
3. measuring the diameter of the field of view and estimating how many cells could fit across the diameter

Well done Class II.  Take note of how much you can accomplish without much direction from me.

Homework

For both classes, your next homework is due Thursday, 9/17.  You are to complete the four magnification questions on the handout given in class (I do not have an electronic copy - hope you didn't lose it!)  Note that these are your first taste of IB-style test questions.  Also, one of these problems could be used as a sample calculation for your assessment statement 2.1.5, regarding magnification.

Best,

Mr. Hill 

Homework Post

R4 and R6 are off pace because we have different lab days, so I'll wait to post about the goals we covered today. 

However, just a quick note that for both classes, your homework is to begin working on your assessment statements for Unit 1.  These should be done in your special marble notebook, and you can refer to the back of your student handbook for Unit 1: Cells.  Check the 2.1 box for what we've been working on today. 

Best,
Mr. Hill

Further Adventures in Brain Science

I just finished reading your comments on Jonah Lehrer's "The Predictions of Dopamine," about the computer that learns from its mistakes.  Many of you expressed surprise that computer programmers would want to model their machines after our meager human brains, and others were relieved to hear that the machine apocalypse in Terminator Salvation wasn't as close as we thought.  The human brain is indeed nature's most powerful tool.  However, one of you had some insight about one way that computers do win out on us meat-sacks: "Unlike computers," this person writes, "humans sometimes don't learn from mistakes and they repeat them."  Good point!  So let's all try to strive to be TD-gammon this year, and zero in on our mistakes.

If you liked reading Lehrer, he maintains a neuroscience blog here: The Frontal Cortex.  Also, the book that we read a selection from, How We Decide, is highly-readable for any level and is chock full of more insight into how your mind works when you're not looking.  Non-required for the course, but I highly recommend it for the curious.

Classroom resources

Today, we worked in groups to examine the "tools of the trade" are available to help them with the considerable workload to follow in IB Biology.

Homework for Monday, September 14th: Complete the online microscope pre-activities in preparation for our first use of the microscope in lab this week.  Please go go to this website, courtesy of the University of Deleware, that offers you two resources: a video introduction to the microscope, and a virtual microscope that you can manipulate and use.  This will help you sharpen your scope skills in preparation for the real thing.  Using these resources, please complete the pre-lab handed out in class.  If you lost it or were absent, the worksheet can be downloaded below.

Microscope pre-lab worksheet

Have a wonderful weekend!
-Mr. Hill

Assessment in Biology

Today, we answered the question: "How will I be graded in Biology?" That's a good question.

All discipuli have hard copies of the syllabus and the Student Handbook, which lay out the expectations for this class, the major assignments that contribute to your grade, and how your grade is calculated.  For reference, you can download those documents here:


Student Handbook

Syllabus

For parents, discipuli, and advisors: please note that on the last page of the student syllabus there is a grade tracker to keep note of your graded assessments and computer your cumulative average.  You can use this tool to keep yourself on track in between term reports.  If you need to update the information in your grade tracker, see me and we can go through your file.

Thanks,
Mr. Hill