Great review website - thanks to Genesis

Hi all, check out this great link for interactive biology animations and tutorials.  Thanks to Genesis for pointing this out!  It has many high quality and informative reviews of the topics we have discussed and future topics.  Definitely book mark this for when you are doing your assessment statements.

Interactive Animation for Biology

Potato Chip = Energy

Today, we examined the burning of a potato chip as an example of the transformation of energy that occurs.  Cell respiration, the metabolic reaction that creates energy from food in our cells, is a variation on that same reaction.  The only difference with cell respiration is that in our body, we "burn slow" - meaning we use enzymes to carefully control the reaction so that we can capture the energy in a useable form.  That form, of course, is our good old friend ATP.


Homework
For homework, you will use the following web resources to investigate how the cell manages energy.  After viewing and reading all the resources, please answer the questions that follow in your class journal and be ready to discuss your findings tomorrow.

Resources:
ATP and Energy Storage
Cell Respiration Video


Questions

1. Draw the generalized structure of an ATP molecule.
2. Explain how ATP is like a "rechargeable battery" for the cell.
3. What type of energy is ATP?  (Potential, kinetic, chemical, thermal, nuclear, gravitational, etc).  Explain your answer.
4. Write the equation for cell respiration.
5. Pause the cell respiration video and draw the chemical structure of glucose.  
6. Where does the CO2 released by cell respiration come from?
7. Where does the H2O released by cell respiration come from?
8. The second video says that energy stored in glucose is like "money in the bank" but energy in ATP is "money in your pocket."  Explain what this means.

Water = Life

Hi all,

Today, we examined the amazing properties of water - that tiny little molecule with the special properties that is the foundation of all life as we know it.  Philip Ball, a scientist whose specialty is water, has said that "Water is life's true and unique medium.  Without water, life simply cannot be sustained."  Water is so intricately linked to life that when astrobiologists go searching for other planets that might harbor life, they follow the water - any planet with liquid water is a likely candidate for life.  Unfortunately (fortunately?), those planets are quite rare.  Most planets either orbit too close to their star, creating high temperatures that cause any water that might exist to boil off, or orbit too far from their star, so that any water that's lying around is frozen and therefore inhospitable to life.  Earth has the "Goldilocks syndrome" - it's juuuuuuust right, wedged in that sweetspot distance from the sun so that our atmospheric temperature is between 0-100C, and liquid water can exist.  And look at all the life we've got!  If we're talking about the stuff of life, water is some important stuff.

Water is oh-so-amazing because of hydrogen bonding, and most of its properties can be traced back to this phenomenon.  Adhesion, cohesion, surface tension, high specific heat, and polar solvency can all be traced back to the strong hydrogen bonds water forms with its own molecules and with other charged molecules like it (we call those molecules that can hydrogen bond with water polar or hydrophilic).  Below, I've posted one of the best animated tutorials on water and life out there - check it out when you have a chance as a review:

Properties of Water Tutorial

Homework
R4 - view animation above, and work on assessment statements.

R6 - revise Lab #1 based on our discussion today, and view animation above; continue to work on assessment statements

Dee Bee Cue

Today we took a practice data based question, or DBQ.  These are by far the toughest IB questions!  But you all did quite well.  We came up with the following strategies for attacking a DBQ:

• Read the paragraph; circle the most important information.  
• Draw the situation to show what's going on if you're a visual person.
• The graph: check the key, label on each axis, title, and units.
• Read the graph with a ruler - and be precise.
• Draw on your knowledge from math to predict and calculate - you have the tools in your head.

Thanks to Genesis, Shaq, and Brian for recording that.

For homework

Complete the take-home DBQ, which will be put in as a 6 points quiz grade.  If you need the DBQ, you can download it here:

Take Home Enzyme DBQ (6 points) 

To complete it successfully, you will need to teach yourself about competitive inhibition.  Look it up in your text, google, or use this web animation:

Enzymes Inhibition Tutorial

Incidentally, you can also introduce inhibitors using the enzyme simulation we used in class (I posted this  two days ago for the curious.)

Best,

Mr. Hill

Enzymes: Life's little helpers

Hi all,

Today we learned about enzymes, the biological catalysts that speed up chemical reactions in the cell.

Check out these animations and videos which offer tutorials about the basic properties of enzymes.  They may be useful as you answer your pre-lab questions for Monday.

How Enzymes Work
Enzyme Action and the Hydrolysis of Sucrase

Homework
R6: Please complete your pre-lab questions for Monday.

R4: There will be a quiz on 6.1.1, 6.1.2, 6.1.4, and 6.1.5 on Monday.  Please note that for the digestive system (6.1.4), you should be able to clearly draw and label the following parts: mouth, esophagus, stomach, small intestine, gall bladder, pancreas, liver, large intestine, anus.  Make sure you can clearly show how the accessory organs (gall bladder, pancreas, liver) are connected to the small intestine.  You can also begin your Unit 2 assessment statements for these numbers, because believe it or not, there are only two weeks left in the term and another unit test is looming!

Thanks,
Mr. Hill

Thanks,
Mr. Hill

Digestive System, part 2

Today, we drew and labeled the digestive system.  Make sure when you do this for your assessment statements that you:

1) Clearly show the connections between each organ.
2) Include the mouth, esophagus, stomach, small and large intestine, gall bladder, liver, pancreas, and anus.

Homework
Check out these animations to review the digestive system.  You might consider starting your new Unit 2 assessment statements!

Organs of Digestion
How Stuff Works: Digestion

Osmosis Jones!

Today, we examined a case of osmosis - the diffusion of water across the cell membrane.  We noted that red onion cells shriveled when placed in water (this shriveling of cell is officially called plasmolysis, and it's the same phenomena that makes your mouth dry when you eat a salty snack and your skin wrinkle when you jump into the ocean).  We inferred that water must have left the cell, traveling along its concentration gradient to create an equilibrium of solute concentration inside and out of the cell.

That's the key thing about osmosis: water will move toward areas of high solute concentration.  Think of it as a balancing act - the high concentration needs to be balanced out by adding extra water (like diluting Kool Aid).

Homework
R4 - mini-quiz on membranes (2.4); also, please research the "missing piece" I gave you and bring in something to share on Monday.

R6 - complete all pre-lab questions on looseleaf or in your journal.  If you lost it, the lab handout can be found here:

Lab 1 - Determining the Concentration of the Cytoplasm

In order to help you with this, you should read textbook pages 89-91 about osmosis and consult the following web resources:

Osmosis Animation (from class - but it's longer)
Similar Osmosis Student Lab (may be a springboard for your ideas)

Please e-mail me with questions at MagisterHill@gmail.com

Unit test next Thursday!

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

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.]

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