Monday, quiz and pineapple wrap up

Today you had your quiz and then we wrapped up the pineapple lab. Make sure you can answer the following questions about enzymes.

1. What are enzymes?
2.What is an active site?
3. What things in the enzyme's environment can denature it?
4. What is the molecule an enzyme acts on?
5. How does the environment affect an enzyme's function?
6. What happens to the collagen in gelatin when you dissolve it in hot water and then refridgerate it?


We then went over the basics of bacterial growth (which is by binary fission).Here is a great site on bacterial growth and the stages.

From the cellsalive site:

LAG PHASE: Growth is slow at first, while the "bugs" acclimate to the food and nutrients in their new habitat.

LOG PHASE: Once the metabolic machinery is running, they start multiplying exponentially, doubling in number every few minutes.

STATIONARY PHASE: As more and more bugs are competing for dwindling food and nutrients, booming growth stops and the number of bacteria stabilizes.

DEATH PHASE: Toxic waste products build up, food is depleted and the bugs begin to die.

Homework for Thursday: Read and take notes on the 13.5 handout and then read the lab for thursday.

Design lab - Enzymes and how they work

On Tuesday you designed your own lab to test if different fruit juices had proteolytic enzymes. Your reasoning was that like pineapple juice, orange, grapefruit, and lemon were all acidic and that could correlate with the presence of the enzyme.

Below is your Protocol
Materials
Pineapple HT/RT, Orange HT/RT, Grapefruit HT/RT, Lemon (pasteurized) HT/RT.
9 Test tubes
Hotplate, beaker with water
Gelatin (source of the collagen)
Kettle to heat water
Thermometer
Clamp
Water
Tape, Marker

Methods
1. Label test tubes (Pineapple HT/RT, Orange HT/RT, Grapefruit HT/RT, Lemon (pasteurized) HT/RT, water)
2.  Prepare Gelatin, mix in 1 packet of gelatin with 1/4 cold water and stir to somewhat dissolved. Then add in 3/4 cup of hot/boiling water and stir till all dissolved. Let cool to RT.
3. Turn on hot plate to high
3. Pipette 3 mL of each juice into appropriate tubes
4. Place the tubes labeled HT into the beaker on the hot plate. When the temp reaches 85C remove the tubes and cool them to RT
5. Add 10 mL of gelatin to each tube (both RT and HT)
6. Place tubes in rack then in fridge
7. Clean up your bench space!


Results!
Below are your results. Can you answer the following questions?

Pineapple design results from lvilleDrFox


1. What claim can you make based on the results and the results from your previous lab?
2. What is your evidence for this claim?
3. How valid is your research? How can you make it better?
4. If you wanted to redesign the experiment, what would you change?

Monday -Design lab

Today we reviewed your pineapple enzyme design labs and chose 2 possible ideas.

1. Independent Variable - juice type (orange, peach, grape, lemon).


2. Independent Variable - temperature (85, 60, 37, 24)

Part of your homework again tonight is to write up the PROCEDURE. You must have it written out when you arrive tomorrow.

Remember to use your original lab as a guide. You need to have a list of all the materials you need and then the steps (i.e. how to make the jello, how much to add to each tube, how many tubes does each group need). AND then a list of the IV, DEP, etc.

example from your original lab

1.      Label test tubes as “pineapple – hot,” “pineapple – RT,” “apple juice – hot,” “apple juice – RT,” and “water.”  Apply the tape at the top of the test tube with a “tail” as shown at right, so steam from the water bath does not remove the labels.

2.      Prepare gelatin in an appropriate beaker.

a.    Dissolve the contents of a gelatin packet in ¼ cup cold water.

b.    Add ¾ cup boiling water to the mixture and stir until completely dissolved.

3.      Pipette 3ml of juice or water into each test tube according to the labels, using transfer pipettes.  Do not cross-contaminate juices by using a pipette in different types of juice.

4.      Place your “hot” tubes in a beaker of water.  Heat the beaker on the hotplate until a thermometer in the water of the beaker reads 85°C.  Carefully remove the tubes from the heat.  Allow contents to come to room temperature (RT).

5.      Add 10 ml ROOM TEMPERATURE gelatin mixture to each test tube.  Use the big pipette for this and do not let the gelatin drip into the green pipetter.  Shake tubes well to ensure mixing of contents

6.      Refrigerate test tubes overnight.

We also reviewed the sickle cell gel electrophoresis handout. If asked could you answer the following questions..
1. What is the phenotype if someone is Aa? Explain
2. What is a recessive allele?
3. How do we use restriction enzymes to determine genotype of sickle cell?

The last part of your homework is the handout below

7 text homework 5 from lvilleDrFox

Thursday - More on Enzymes

Thursday we worked on the lab involving how proteolytic enzymes and/or heat affect proteins such as collagen. Collagen is a structural protein involved in skin, connective tissue and bones of animals. Below are a couple of images of collagen and how it is organized.

Enzymes have specific 'substrates' or targets on which they work. Some enzymes 'digest' or 'break down' their substrate, while others put 2 targets together. Which type is our 'proteolytic' enzyme from fruit? What is the enzyme's substrate in our lab? Will that enzyme break down another substrate?

Proteins (which is what enzymes are!) can be denatured by heat and some chemicals. This is the process of denaturation.

In our lab, we are looking how 2 variables affect

Final bits on digestion

We finished up the small intestine and reviewed the rugae of the stomach (these are the folds that expand when food is eaten and help with mechanical digestion in the stomach). Side note: The stomach can actually absorb aspirin and alcohol.


We also discussed how pepsin in the stomach is a positive feedback loop. Pepsin is an enzyme in the stomach that breaks down proteins into "medium size" molecules called peptides (what do you think pepsin's optimal pH is?). These peptides in turn trigger the production of more pepsin thereby speeding up the digestion of the larger protein molecules (Why is this important?).

After we leave the small intestine where food is completely broken down and absorbed (this happens near the end), we move into the colon (or large intestine). The structure of the colon is shorter but with more diameter than the SI. In this organ, water is absorbed into the bloodstream via capillaries. This causes the waste to become bulkier. (why wait until the end to absorb water?). The bile that was provided by the liver to the small intestine, causes the waste to turn brown when the water is taken out.

Why is fiber important?

From the colon we move into the rectum (storage organ for waste, until it can be released) and finally to the anus where waste exits the body.

Can you identify what organs mechanical and/or chemical digestion occurs? What are the enzymes involved in each stage and where are they made?

Enzyme animations link

I would like you to review this website on Enzymes, it will help clarify a few things!

Enzyme Animations

Here are a few images of enzymes to help explain function:

Thursday and Monday -Digestion

Thanks to Mrs. Saxe for going over BMI with you. Here is a site for you to explore more on BMI. You also went over how the liver is involved in digestion.

How is the liver involved - produces bile (an emulsifier) stored in the gall bladder and moved into the small intestine. The bile increases the surface area of fats by mechanical digestion. Here is a website with an animation on bile and fats (Bile site)

We continued on our journey through the digestive system. We are still in the small intestine.
What is the function of the small intestine? = breakdown of food and absorption of simple sugars, amino acids, fatty acids, nucleic acids, vitamins, and minerals?


Pancreas enzymes (amylase, lipase, protease) and: (where are these used?)
DNAse breaks down DNA into nucleic acids (where does the DNA come from in your food?)
Where are the nutrients then absorbed into? The plasma! since there are capillaries within the Villi in the small intestine.

What are villi? Finger like projections that help increase the surface area to increase nutrient absorption into the blood. Villi have capillaries within them.

Villi have microvilli on them - to increase the surface area even more for nutrient absorption.

How does the digested food move through the small intestine?