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!