Negative Feedback Loops

Today, we finished discussing the circulatory system and started our last topic for this unit, homeostasis.  We discussed a specific example of a negative feedback loop that maintains a constant temperature in your body.

Homework
For homework, you will read about the negative feedback loop that maintains a constant blood glucose level in your body.  Please read p.768 in your text and answer the questions that follow in your journal:

1) What is glucose and why is it in your blood?

2) Insulin and glucagon are hormones.  Flip to page 758 and read the section "Hormones are Chemical Signals."  Referring to figure 42.2, explain what a hormone is and how it works.

3) Copy the diagram of the feedback loop on p.768 into your notes.  Using the terminology we discussed in class, label the SENSOR and EFFECTORS.

4) What does it mean that insulin and glucagon are antagonistic hormones?

Blood Vessels of the Circulatory System

Today, we looked at an overview of the circulatory system.  Tomorrow, we will be comparing the three types of blood vessels - arteries, veins, and capillaries.

Homework
For homework, please research  these blood vessels and complete three structure / function charts - one for arteries, one for veins, and one for capillaries.  You may do this in your notebook, and we will discuss it first thing tomorrow - make sure you come to class ready!

You may uses the text reading handed out in class, and in addition the following web resources are available.  Do consult all of them for maximum comprehensiveness.

Merk Manual - Veins
The Human Heart at the Franklin Institute
http://www.ivy-rose.co.uk/HumanBody/Blood/Blood_Vessels.php

Lab #3 Due Tomorrow

Hi all,

Make sure to complete Lab #3, a Design and Data Collection section, for tomorrow.  E-mail me a single word document by tomorrow or bring a paper copy to class.

Missing DBQs

The following discipuli owe me take-home DBQs from Friday.  Hand in tomorrow, or it's a zero!

AMIR
MRIDUL
JAVIER
SHANIQUE
PEDRO

The Resp...er... Ventilation System

Hi all, today we learned how to draw, label and annotate a diagram of the ventilation system of humans.  You should be able to include the following structures in your drawing - trachea, bronchi, bronchioles, lung tissue, diaphragm, and finally, starting tomorrow, the alveoli.

Homework
For homework, google "alveoli" or look them up on p.676 in your textbook.  Draw the alveoli as a nested picture in your drawing of the ventilation system that you completed in class today.  Also, write three structural features you notice about the alveoli.

DBQ

Hi all,

Really good work today on the DBQ.  Especially R6.  Everyone really brought their A-game to class today.

Many of you expressed worry along the lines of "my gosh - on an exam I would not be able to spend 40 minutes talking to my peers about the experiment before I answer the questions!"  That is true.  However, rest assured that the more of these you do, the better you will get at them and the more natural it will feel.  We're all on the right track to success.

Homework
Do complete the DBQ questions for homework.  Pay attention to the point values and provide sufficient depth.

Your lab due date has been moved to next Thursday.

Next week I will be holding special office hours Monday and Wednesday to look at drafts and help you in writing your lab.

DBQ Tomorrow

Hi all,

Tomorrow, we're going to have another DBQ.  Remember the DBQ strategies we discussed:

1. Describe every part of the graph!  
2. Use a table of comparison to compare two different data series on a graph.
3. Use unpacking when you see the command term EXPLAIN to make sure you provide sufficient molecular / cellular detail about what is causing the observed changes.
4. Use a ruler to read the graph.

The DBQ will give you an experiment based on cell respiration, lipids, and carbohydrates.  You will want to review this information for tomorrow, because the more you know the better prepared you will be to understand the experiment!

Lab 3 (Yeast Lab) Data

Hi all, below please find your raw data from the probes.  Right click on your link and select "save as" to download the file.

Happy graphing!

Jafar and Ryan
Anabel Lillian and Javier
Mridul Tyson and Billy
Amir Pedro and Brian

Spencer, Zehra, and Kai Ni and Victoria and Megan, I am having some difficulty uploading your files - I will e-mail them to you at 2:30 today.

Thanks
Mr. Hill

Synthesis

Today, we examined synthesis reactions - the process by which the cell makes larger molecules.  This can be used to store food for later, as in the case of synthesizing a polysaccharide like starch or glucose; or, the cell can use synthesis to build functional or structural molecules - for example, synthesizing an enzyme or membrane protein from amino acids, or synthesizing a phospholipid from fatty acid tails, glycerol, and a phosphate.  With synthesis, the cell can build whatever it needs from the raw materials taken in from digestion.  Ian B. made a really good connection to digestion today, pointing out that we humans eat big polymers, break them down into monomers so they are small enough to cross the cell membrane into the cell, and then the cell uses synthesis to reconstruct the polymers inside it.  Pretty cool!

Homework
1) On looseleaf, write a response to the prompt we discussed in class: Explain the role of enzymes, activation energy, and ATP in the synthesis of a disaccharide from two monosaccharides [6].  

2) Your post-interim assignment is due Monday.

Best,
Mr. Hill

Carbs and Lipids

Today, we talked about how the molecular structure of carbs and lipids is related to their properties.  We talked about carbs, looking at the example of the monosaccharide (or simple sugar) glucose:

And we looked at a triglyceride, a molecule of fat composed of glycerol and three fatty acids:

You should be able to discuss the molecule in relationship to their polarity, energy capacity, and readiness to break down via respiration.

Homework

Read textbook pages 138-141 about monosaccharides, disaccharides, and polysaccharides, and answer the following questions in your journal:

1. Name two examples of each of the following: (a)monosaccharide, (b)disaccharide,  (c)polysaccharide
2. What's the difference between a monosaccharide, disaccharide, and polysaccharide?
3. Draw a picture of a condensation (dehydration synthesis) reaction between two monosaccharides to make a disaccharide.  Label the atoms that are removed and the new bond that is formed.
4. When you eat a candy bar, some of the glucose you take in is respired immediately, and some is synthesized into larger chain molecules (polysaccharides).  Why would your cells bother to synthesize a polysaccharide?

NOTE!!  I am missing the "Art of Explanation" unpacking take home quiz from last Friday for the following students:

IAN
JAFAR
GENESIS
BRIAN

If you have this, please hand it in tomorrow otherwise it's a zero!

Anaerobic and Aerobic Cell Respiration

Today, we debriefed cell respiration a little and then learned how cell respiration can be used to explain two phenomena that occur when we are very active: heat and soreness.  In lecture, we revealed two new facets of cell respiration:

1. The energy transfer is inefficient (about 60% efficient, to be precise)
2. Respiration can be aerobic (using oxygen at a higher energy yield) or anaerobic (no oxygen, lower energy yield).

(R6 - we're going to do #2 tomorrow, no worries)

Homework - do on a separate sheet of paper, to be collected

R4 - Respond to the following prompt on a separate sheet of paper, and treat it like a short answer.  This means you should unpack it, and then repack in written form, to get a lot of detail!

Prompt: Explain why anaerobic respiration yields less energy than aerobic respiration. [4]

R6 - Respond to the following prompt on a separate sheet of paper, based on our discussion today.  Treat it like a short answer - meaning you should unpack it, repack it in written form, and give a lot of detail.

Prompt: Explain why activation energy is only required once, at the beginning of cell respiration. [4]

Cell respiration model

Hi all,

Today in class we debriefed your homework and described the structure of ATP, and then went on to model cell respiration.

When you think of cell respiration, think about it as coupled reactions.  The rule of thumb is: break a bond, make a bond.  Meaning, when you break a bond in glucose and release the potential energy stored within it, you have to capture that energy; to do so, you have to make a new bond - for example, a new phosphate bond between ADP and Pi.  Now, that energy is captured and stored again, ready to use for the cell.

Homework
I had planned a lecture for tomorrow, but I'm going to adjust the schedule in order to give us a little more time to discuss what happened in class yesterday.  For tonight, take a break, or continue working on your post-interim assignment, due Friday.

Thanks
Mr. Hill

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.

The Art of Explanation

Hi all,

On Friday, we looked at unpacking, a strategy to maximize the depth of explanation in a short response.  This works best when you see the command term explain on your IB exams.  The goal is to give a lot of depth at the molecular and cellular level about what's going on.  To use this strategy on a short answer:

1. Identify key concepts the question is asking about.
2. Unpack those concepts by brainstorming everything we learned in connection with them.
3. Draw a model of what's happening at the cellular or molecular level.
4. Repack your explanation into a few concise, deep sentences explaining the phenomenon.

For example, in the prompt "Explain the necessity of enzymes in digestion"

I would "unpack" the terms enzyme (biological catalyst, lowers activation energy, speeds up reactions, breaks down bigger molecules into smaller molecules, acts on a substrate, examples are amylase, pepsin, lipase) and digestion (break down of big molecules like polysaccharides, polypeptides, and fatty acids into smaller molecules, absorption into blood stream, smaller molecules diffuse into cells, where they can be respired).  I can use this information to now answer the question in greater depth.

For homework:

"Repack" the examples we looked at in class, writing your deep explanations.  This will go in as a take home quiz grade, so do a good, thorough job.  If you are missing the sheet, the questions are:

1. Explain, with an example, the necessity of enzymes in digestion.
2. Explain the effect of pH on enzyme activity.
3. Explain why the rate of glucose uptake by facilitated diffusion (on the DBQ) levels off after an external concentration of 450.
4. Explain the importance of the tertiary structure of proteins to membrane ion channels.

Below is the graph for #3 for those who may need it.  Thanks to Kai Ni for pointing this out!

On Monday, we're moving onto our next topic: cell respiration (whoo!)

Best,

Mr. Hill

Back in Bio

Hi all,

We're back and we survived our first round of interims!  Congratulations!

Homework
Please complete the interim reflection template and prepare it to hand in, with your interim, tomorrow.

Note that you are only selecting what post-IA assignment you want to do; it will not be due until next Friday.  I am going to look over your decisions over the weekend and approve them.

Virtual Office Hours for Interim

Hi all,

I will be conducting virtual office hours on this Sunday, Nov. 8th, from 7PM-9PM.  Good luck studying for your interim!

For your interim, please remember to bring

1. Your assessment statements to hand in
2. A calculator
3. A ruler
4. A pen and pencil

Best!

Mr. Hill

Virtual Office Hours

Hi all,

We'll be trying something new to offer you some support in preparing for your unit exam.  This Sunday, from 8:00PM - 9:00PM, I'll be conducting virtual office hours to address any last minute questions you have about our stuff of life unit.  If you'd like to take advantage of this, you can instant message screen name MagisterHill on AIM.  Make sure to tell me who you are.

I will have an away message up if I'm working with another student.  If I have an away message, IM me with your question and I'll take your questions in the order that I get them.

Hope this is helpful.

Best,
Mr. Hill

Protein Folding

Hi all,

Today we looked at protein folding using three examples (silk / hair, amylase, and hemoglobin).  We saw how proteins assume complex shapes based on the properties of their amino acids, particularly their R-groups.  I'm posting the lecture notes below, but I would also recommend you take a look at a few animations.  Folding is a dynamic process, so it helps to look at a video:

Video resources
Protein Folding Interactive Tutorial
Short Protein Folding Animation

Here are the lecture notes: Protein Folding Lecture Notes

Homework
DCP write-up for Lab #2 (enzyme catalase and temperature) is due Friday.  Please check the blog post for your data if you haven't already.  If you need to find it, click the "labs" link on the right hand side under Buckets, and then find the post with your data.

Best of luck!
Mr. Hill

Amino Acids

Today, we discussed the chemical structure of an amino acid, the building blocks (or monomers) that make up proteins (a polymer).  An amino acid looks like this:

Notice the amine group, carboxyl group, and that pesky R-group, the wild card that is different for every amino acid and determines its properties.  There are about 20 different amino acids, all with their own R-group:

That'a a lot!  Notice that some are negatively charged, some are positively charged, some are polar, and some are nonpolar.

We can join amino acids together by dehydration synthesis, also called condensation, which looks like this:

Or, reverse the process and do a hydrolysis reaction, liberating two individual amino acids.

These are the fundamental mechanics of building a polypeptide, or protein; tomorrow, we'll look at protein folding, the dynamic molecular dance that occurs when a long polypeptide chain assumes its complex shape.

Homework

In preparation for our lecture, please pre-read pages 146-149 about protein structure.

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

Unit 2 Exam is one week from today

Today, R6 demonstrated the properties of water and R4 learned a little bit more about Microsoft Excel to help them rewrite their lab reports.  Tomorrow, I will be posting a big post about water with some helpful review material.

Note that today is one week until your unit 2 exam, and two weeks until your first interim assessment.  The time to review is now!  I'm posting an outline of the rest of the week, with relevant assessment statements for each day.

Monday / Tuesday - Properties of Water Demos and Discussion (3.1.4-3.1.6)
Wednesday - Whole Class Modeling of Polypeptide Structure (3.2.5)
Thursday - Lecture on Protein Folding (7.1)
Friday - Organic and Inorganic Stuff Share Out / Exam Review (3.2.1 and 3.1.1-3.1.3)

Next Monday - Unit 2 Exam
Next Wednesday - Unit 2 Exam Review and Interim Assessment Review

Homework
R4 - Please revise your Lab #1 to turn in tomorrow.  You must hand this in when you walk in tomorrow.

R6 - Continue to work on assessment statements, due the day of the Interim Assessment.

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

Fitting a football field inside of you

Hello all, today in R6 we looked at the microscopic structure of the small intestine, an organ so folded up and crammed full of surface area that, if we could unfold it, it would stretch about the distance of a football field.  We connected the large surface area to its role in absorbing digested nutrients into the blood.  More surface area means more contact space for absorption.

Here are some micrographs of the interior of the stomach:

Finally, here is an electron micrograph of a single cell that lines the villi.  Notice that the cell membrane is folded as well - we call these folds microvilli:

So much surface area!

Homework
R4 - complete assessment statements 6.1.3, looking up data about three enzymes.
R6 - continue to work on assessment statements and lab #2

Everyone should download their lab data and read the post below, which has information you need to successfully complete your write-up.

Lab #2 Data

Hi all,

I'm going to post a series of links containing your raw data from Lab #2.  A few important points:

1) The data appears as a columns of numbers, unlabeled.  Your first run is on the left hand column; your second run will be next to it; and so on.  You will need to label each run.

2) The data as it appears is NOT in an acceptable format for the lab write-up.  You must add table headers and borders so that the data table conforms to conventions in the student handbook.

3) The graph did not export.  You must choose an appropriate way to process and graph the data, drawing on your experiences in the post-lab discussion and the following days (for example, we calculated the rate and discussed several ways of graphing in class when we used the simulation).  You should be able to explain why you made the graph choices you did.

A good rule of thumb is that your presented data should answer the question you are investigating.  I should be able to look at your graph and see the answer to the question "how does temperature affect the rate of an enzyme controlled reaction?"

Labs are due next Wednesday.

Your files are posted below.  [UPDATE: TO DOWNLOAD THE FILE, YOU MUST LEFT CLICK AND CHOOSE "SAVE LINK AS," AND SAVE THE FILE TO YOUR COMPUTER.  IT WILL BE A .CSV FILE, WHICH YOU CAN OPEN AND VIEW IN EXCEL.  THANKS]

Amanda Jose James
Adrian Ryan Jafar
Shaq Ryuichi Kenny
Zehra Spencer Kai Ni
Amir Brian Pedro
Romi Jerry Arisbeth
Harry Genesis Kazi
Mridul Tyson Billy
Javier Anabel Lillian
Jennifer Ehis Lourdes
Victoria Megan Shanique
Lawrence Brittany Ian Giselle

See me with questions.

D-Day 2009 (Denaturation Day)

Hi all,

Today, both classes examined how enzymes denature, or lose their shape, when they are exposed to pH or temperatures outside of their comfort zone.  Anything that interferes with the delicate molecular structure of an enzyme can denature it, ruining them!  One interesting thing about denaturation is that it's irreversible.  If you had taken the enzymes that you heated up to 80C in your lab and cooled them down to room temperature again, you'd still see no reaction - the enzymes were cooked for good.

This has a lot of practical applications - for example, when you cook your food, you're applying intense temperature and kinetic energy to any bacteria hanging out on the food.  Their enzymes denature, the bacteria die, and when your food cools down to a reasonable temperature to eat, the bacteria are dead - for good.  Phew.

Here is the enzyme simulation we used in class today - it's pretty helpful so come back to it for review: Enzyme Substrate Simulator

Homework
R6 - quiz tomorrow on 6.1 (digestive system).  Please also make a note of doing 6.1.4 for yourself - look up three enzymes and be able to name their source, substrate, and optimal pH and temperature for activity.  Amylase and pepsin are two good ones to start - the third enzyme you can pick.

R4 - continue to work on assessment statements.

I apologize to everyone, but I'm having some technical difficulties so I won't be able to post your lab data until tomorrow.  You can expect it by 5:00 tomorrow night.

Lab data - coming tomorrow

Hi all,

Sorry for the delay, but I won't be able to post your raw data until tomorrow.  Check back then and I will have everyone's files up so that you may do your write-up.

Homework
R4 - you guys have a day to work on your assessment statements - either revising old ones or continuing on Unit 2.

R6 - please look up denaturation in the textbook, write a description in your notebook, and bring that with you to class tomorrow.

Thanks,
Mr. Hill

Enzymes galore!

Today, R6 completed their lab #2 about how temperature affects enzymes.  R4 examined the microscopic structure of the small intestine.

Homework

R4 - please complete pre-lab questions for tomorrow.

R6 - Tomorrow we will discuss you lab data.  In preparation, please look up denaturation in your textbook - you may find it enlightening to some of the results you saw today.

Course Update! Important!

Hi all,

I've been reviewing the syllabus calendar for Unit 2 and I have some changes to make regarding the schedule.  This affects which assessment statements you have to do and when they are due, so please mark the following changes down in your student handbook in the assessment statements for Unit 2:

1. Your unit 2 exam will be in class on Nov. 2nd.  However, we are not going to completely finish Unit 2 before this date.  As such, the Unit 2 exam will cover ONLY: 3.1 (elements and water), 3.6 (enzymes), 7.5 (proteins), and 6.1 (digestion).  We will spend an extra week on 3.2 (carbs, lipids, proteins) in term 2, but you are not responsible for this material for the exam OR for the interim assessment.
2. Because the unit 2 exam and interim assessment are quite close to one another, I will not be collecting your assessment statements until the day of the interim assessment.  Please plan on handing them in again on Nov. 9th before your interim.
3. Please cross out the box for 7.6 (Enzymes AHL).  We will not be doing this material until next year.

Thanks,

Mr. Hill

REMINDER - Micrographs Extra Credit Assignment Due Mon.

Hi all,

Just a reminder that if you are undertaking the micrographs extra credit assignment, it is due Monday, and can net you up to 5 extra scaled points on your most recent Unit Exam.  I highly recommend everyone take this on!  Scroll down to last weekend's post for more information about the assignment.

Thanks,
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

Duh-gestion

Today, we built a working classroom model of the human digestive system, and observed how large food particles can be physically and chemically digested into molecules that are small enough to be transported into the cell.  This is just the tip of the iceberg of our second unit, about the "stuff of life" - the matter, molecules, and atoms that all living things are made of.

Homework
Your osmosis lab report is due Thursday.  In class, we discussed the following in regards to that assignment:

1. It is a DCP write-up - three sections of the full report are required (raw data, processed data, and presented data).  
2. Use all the resources available to you in the student handbook, including the anchor paper, the checklists, and the guidelines for tables and graphs.
3. The assignment should be typed, or it will not be accepted.
4. This is an individual assignment.  Even if you have the same data, your own write-up is expected.

Thanks!

Mr. Hill

Make Robert Hooke Proud

[NOTE: for the take-home quiz assignment, scroll down to Friday's post]

As a class, we really bombed out on the micrograph question on the exam.  Oops.  

So now, as a class, we have an opportunity to learn and grow from that oops.  Your assignment, if you choose to accept it, is to create a portfolio of micrographs of each of the organelles that we have studied.  And, if you choose to accept it, your efforts will be rewarded with up to 5 scaled points back on your Unit 1 exam. 

If you embark on this journey of retribution, you will:

• Use the internet to collect micrographs showing the following organelles: plasma membrane, nucleus, mitochondria, chloroplast, golgi apparatus, rough endoplasmic reticulum, and lysosome.
• For each organelle, show several labeled micrographs pointing it out.
• In writing, explain how you would identify the organelle in an unlabeled diagram.

This assignment, if you choose to accept it, is due Monday, Oct. 19th.  It may be typed.

Biology = Awesome

Just stumbled upon this article from Wired magazine, which is chock full of amazing, real images that biologist have accrued with their powerful microscopes.  Apparently, lens maker Nikon holds an annual competition for the best photo produces through microscopy.  The article has the best of the best from the past 35 years - very cool.  Check it out!

The image above is a double transgenic mouse embryo - it looks like both the developing mouse (in pink) and the mother's placenta (green) have been genetically altered to glow their fluorescent colors under the microscope.  Incidentally, that's the same technology a team of neuroscientists used to make the nerve cells appear rainbow colored - as in the image that makes up the blog's banner.

In another note, I have made an executive decision to give everybody an opportunity to recoup some points on their unit exam by doing a little research on microscopy... more details to come on Tuesday.
Enjoy your three day weekend!

Take home quiz!

NOTE: PLEASE COMPLETE THE BRIEF POLL AT THE RIGHT.  


Today we reviewed the exam and went over strategies for constructed response questions.  Some pointers:

1. The number of points indicates how many "informational nuggets" you need to dish out.  [total 8 marks] means you need to provide at least 8 distinct pieces of information to get full credit.
   
2. You don't lose points for incorrect or irrelevant information - so it's better to hedge your bets and put as much information down as you reasonably can.
3. You have freedom to construct your response how you want - bullet points, a chart, a table, a diagram, or narrative prose can all be excellent ways to respond depending on the question and your strengths.
4. If you have the time, be elegant - because especially high-quality responses can earn you up to two extra "bonus points" that pull up your overall score or compensate for a lack of information.
   

A take-home quiz is the consummate gift to you: a chance to recoup or maximize your quiz grade and a chance to practice the art of the constructed response - all with ample time at your disposal so that you may put the maximum of effort into your endeavors.  If you don't get at least a 100%, it will be because of your laziness, not your intelligence or test taking skill.

So, your assignment for Tuesday is:

On unlined, white paper, hand write a constructed response to the following prompt:


     1.  Explain the various methods cells use to transport materials across membranes. (Total 8 marks)


You might look back at the lecture notes for cell transport (posted online), your class notes, and the textbook for resources.

Also, please remember that your DCP write-up for our osmosis lab is due Wednesday.  Late papers will not be accepted.

Thanks!

TD-gammon's first match...

Hello all,

To inspire you while studying for your first unit exam: Click Here!!!

Just a reminder on testing protocol tomorrow:

1. Bring a pencil, pen, ruler, and calculator.
2. Enter the room silently and ready to work.
3. Drop off your assessment statements at the table on your way in.
4. Sit wherever there is a test and begin immediately.
5. You must finish in 40 minutes - get there on time!!!!!

See you tomorrow!

Lab work, continued

R6 peer reviewed data today; R4 started their osmosis lab.

Homework
R6, please look up your missing pieces and prepare for the Membranes Quiz (2.4).

R4, please e-mail me your data tables and graph at magisterhill@gmail.com before 8AM tomorrow.  

Labwork

R6 completed their first investigative work today; R4 will begin tomorrow.

Homework
R4 - answer pre-lab questions for tomorrow on looseleaf or in journal.  Scroll down to post from Friday for web resources to help you.

R6 - your group must send Mr. Hill via e-mail (magisterhill@gmail.com) by 8AM tomorrow morning:

• raw data table
• presented data (a graph)

Please send these either in microsoft excel or word, as attachments.

The purpose of this is so that we can discuss people's data and choices.  Your final draft of a "DCP" (data collection and processing) section of a lab report will be due next Wednesday.

Practice identifying cell parts in micrographs

Boston University has an excellent catalog of electron micrographs that highlight the different cell parts.  This is great practice for you in identifying cell parts.  The site can be found here:

BU Histology Catalog

If you scroll down to where it says "know the structure, function, and location of:", it lists different organelles.  If you click on the arrow next to each organelle, it will take you to an annotated micrograph pointing out the organelle.  

Note that this resource comes from the BU medical school.  I hope that gives you an idea of the caliber of the IB program - we need doctoral program resources to tackle it!  This is good.


[Note - if you are looking for the pre-lab homework for lab#1, scroll down to the post for Friday, Oct 2]

Cell drawings for assessment statements

There was a question on the parking lot about what your cell diagrams should look like for assessment statements.  I found an exemplar to give you an idea:

Unlike the electron micrographs, you cannot simply cut and paste this in your notebook.  Rather, you should be able to draw and label a diagram of a generalized cell like this on the spot, from memory.  You may very well see a question on your exams that instructs you to do this.

Special Office Hours Sessions Next Week

Hi all,

I recognize that next week is a big biology week for everyone, with the unit test and assessment statements being due on Thursday.  As such, there will be two special office hours sessions to assist you in your endeavors:

Monday, Oct. 6th (2:30-3:15): Assessment Statements Workshop
Don't know what an assessment statement is?  Confused about the difference between objective 1 and objective 2?  Want to check your work or see examples of excellent assessment statements notebooks?  Drop in on Monday afternoon and we'll work it out.

Wednesday, Oct. 7th (3:15-4:00): Unit 1 Review Session
Practice problems, content help, and group study - be there or be square.

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!

Cell transport

Today, we had our second "college-style" lecture.  I discussed four types of cell transport:

• Simple Diffusion
• Facilitated Diffusion
• Active Transport
• Endocytosis / Exocytosis

All these types of cellular transport are dependent on the wacky, weird fluid mosaic nature of the membrane - that it is both a solid barrier and a fluid, bendable, mendable, breakable substance.

By popular demand, I have posted the Powerpoint as a PDF.  You can find it here: Cell Transport Lecture

I have also gone back to my post about the Endomembrane System and posted the Powerpoint.  You can now find all Powerpoints by clicking on the "Lecture Notes" label in the buckets app at the right side of the blog.

Homework

For homework, consult textbook pages 92-95 in order to do you assessment statements based on the lecture.  You should be able to complete 2.4.5-2.4.8.

NOTE: All classes meet in the lab tomorrow.  Report directly to lab!

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

Welcome to IB Biology!

Greeting to Class II discipuli and their parents, guardians, siblings, family pets, and all others who are joining us for the inaugural voyage of IB Biology!

The International Baccalaureate and the Brooklyn Latin School are proud to offer an intense two-year course in Biology, the scientific study of life.  Throughout our journey together, this blog will serve as a home base and study resource for discipuli and their families alike.  As we progress, I will be updating the blog with course information, upcoming deadlines and test dates, study material, helpful animations and videos, and just plain ol' fascinating biology stuff for the curious.  Discipuli, I recommend you bookmark this page and check it regularly.

To parents: I'm often asked how you can help your child succeed in my class.  Maybe some of you are expert NASA trained scientists, and maybe some haven't looked at science since you accidently blew up the chemistry lab in high school.  Both are great, as is everything in between.  Regardless of your background, the best way you can help your child (and me!) is to talk to them regularly about what they're learning in biology.  The more they talk and think about this stuff outside of class, the better it sticks.  And let's face it, biology is fascinating!  You're invited to check the blog regularly if you want to find out more about what we're learning, or if you want to check up on upcoming tests, quizzes, and other assignments.

I'm looking forward to working with everyone over the next two years.