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

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

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.

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.

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