Metabolism

Essential Biology Learning Guides (homework, review)

Metabolic Processes
3.6/7.6 Enzymes (including AHL on Enzymes)
3.4/7.2 DNA Replication (including AHL on DNA Replication)
3.5 Transcription and Translation (core material)
7.3/7.4 Transcription and Translation (AHL material)
3.7/8.1 Cellular Respiration (including AHL material on Cellular Resp.)
3.8/8.2 Photosynthesis (including AHL material on Photosynthesis)

Support material for unit (homework, class discussion)

Metabolism
Topic 3.6/7.6 powerpoint (S Taylor) CJ Clegg text pp. 52-62 & 261-267
Topic 3.4/7.2 powerpoint (S Taylor) CJ Clegg text pp. 66-68, 240-243
Topic 3.5/7.3-7.4 powerpoints (S Taylor)
note that there are two separate sets of slides - one for SL(core) material and one for HL (additional HL) material
CJ Clegg text pp. 69-74, 243-253
Topic 3.7/8.1 powerpoint (S Taylor) CJ Clegg text pp. 76-82 & 269-276
Topic 3.8/8.2 powerpoint (S Taylor) CJ Clegg text pp. 82-90 & 277-293

(Here's an extra slideshow on photosynthesis that I assembled similar to the "spaced learning"
document that was available for respiration)

3.6/7.6

Enzymes

prezi to review water/carbs/lipids/proteins/enzymes both SL and HL

two great animations, used in class but worth another look for review...

This does an especially good job of illustrating allosteric enzymes and their regulation

Use this to convince yourself of the trends in graphs showing the effect on enzyme activity by (1) pH, (2) temperature and (3) substrate concentration. Also a great way to see the reasons behind the effect of inhibitors.

Here's a short treatment of the progression of scientific thought about how enzymes work...and the change form an earlier simpler model (Lock and Key) to a newer more complicated (Induced Fit) idea. (click image to increase size)

Lactose Tolerance - a preview of evolution and an application of biochemistry

3.4/7.2

Animation showing the detail of DNA replication

Another fine animation from Giannini at St. Olaf...Once you are comfortable with all the different "players" in this mechanism, label and color code the p99 7& p101 in Biozone workbook.

How do we know that DNA replication is semi-conservative?

Click on the pictures of Meselson and Stahl to see their experiments that verified this mechanism for DNA replication. Then try DBQ 2 below.

Here are three DBQ's from the Biology course Companion Book...complete them as though you were taking an exam...paying close attention to the command terms.

DBQ 1

DBQ 2

DBQ1 (answer)
1. The sugars are different (ribose v. deoxyribose); RNA contains uracil while DNA contains thymine
2. DNA is double stranded while RNA is single stranded3. DNA RNA
Double stranded Single stranded
Contains deoxyribose Contains ribose
Contains thymine Contains uracil
4. Both are polymers of nucleotides/nucleic acids; They both have the bases adenine, cytosine and guanine; The sugar in both is a pentose; Both have a backbone of phosphate-sugar- phosphate.

DBQ2 (answer) ALSO SEE THE ANIMATION DIRECTLY ABOVE
1. A DNA molecule composed of only N-14 should have a peak at 1.710.
2. After one generation grown in N-14, there was no peak at 1.710.
3. Therefore replication is not conservative.
4. If dispersive, no matter how many generations, all molecules would have same ratio of N-14 to N-15.
5. Not dispersive as there would always be only one peak and second generation grown in N-14 has two peaks.

DBQ3 (answer)
1. More radioactive fragments of all sizes at 30 seconds; Increase in ratio of larger fragments to smaller fragments at 30 seconds/2 peaks at 30 seconds versus one peak at 10 seconds.
2. Two peaks suggests two different sizes of molecules predominate;
Higher peak represents large number of small fragments/lagging strands;
Smaller peak represents a number of longer fragments/leading strands.
3. If lagging strands are joined together by DNA ligase, then the number of initial small molecules would decrease and the number of larger molecules would increase. This is what is observed so the hypothesis is supported.

Bio Song

Listen to my explanation
Bout to teach you replication
Get ready cause this is how it goes

First start with breaking the bonds
The base pairs should correspond
The helicase does split the strands
Where it starts is the origin

Start the splitting by rich A T
That’s because only two bonds between
Can’t start by C and G
Bonds between are more like three

Get ready for the important step
You can already guess what’s next
That’s right RNA Primase

They draw RNA nucleotides
Which then bond to DNA side
This is due to the hydrogen bonds
In which the base pairs should correspond

Listen to my explanation
Gonna give you a education
Between me and you no stipulation
Please don’t hate cause that good sensation
Tryin’ to teach you replication
Please be still, please be patient
C-C-C-C-Cause I don’t repeat myself

Listen up we’re halfway through
Pay attention know what to do
Don’t go stress have some fun
It’s only a final, ah where done

To pick up from last time
The leading strand is doing just fine
The lagging strand 3 to 5
Can’t be read can’t go thrive

It needs help in this case
From a friend RNA Primase
The two RNA create a gap
Called Okazaki Fragments, Oh snap

I need so much help yea, please someone help me
Yet I feel good bout this test, Oh I guess we’ll see
This bio thing is real hard, I kinda get it
Just in case I wrote this song, extra credit

Remember those gaps from before
They are removed they are no more
This is thanks to a good ligase
And don’t forget DNA Polymerase

New double helix is consisted
Of old and new chains that are twisted
Two big words, no abbreviation
Semi-conservative replication

The last step, not to late
Is to finish, to terminate
Then all fixed errors are complete
Remember these steps, then repeat

Listen to my explanation
Gonna give you a education
Between me and you no stipulation
Please don’t hate cause that good sensation
Tryin’ to teach you replication
Please be still, please be patient
C-C-C-C-Cause I don’t repeat myself

R Serra, '11

3.5/7.3-4

#1 Basics of Transcription

Be able to name and explain function of each element shown.

#3 Basics of Translation

Every labelled element is required except the names of the three binding sites on the large subunit of the ribosome.

#2 getting into some HL detail...

One BIG difference between prokaryote and eukaryote protein synthesis is the role of intron splicing exclusively in eukaryotes. Read the intro and conclusion carefully and work through all the sections of this animation.

And for those really serious - a research review of transcription by an expert.

21st century graphics...transcription and translation

then, the ultimate re-enactment video...prepare yourself (mid century graphics??)

For reference - Codon Usage Chart - Universally applicable.

Prezi of the combined processes of transcription and translation. Begins with overview and then details of each process.

3.7/8.1

Cellular Respiration

Now we can really start to make some connections - the study of cellular respiration will demonstrate a process that links the importance of
(1) the ATP cycle to drive enzymes and active transport across membranes,
(2) lysis, synthesis and modification of biomolecules - think breaking down carbon compounds like glucose, pyruvate, formation of new products,
(3) how organelles specialize in order to optimize the functional use of particular structures within organelles.

Let's start with the following introduction, courtesy of Crash Course Biology -

Respiration diagrams for annotation...

A thing of beauty...

Animations to break down Electron Transport:

Prep for respiration quiz...answer key to final questions on EB3.7/8.1. Click here.

Prezi for reviewing respiration, introducing photosynthesis

what it's all about?

3.8/8.2

Photosynthesis (Topics 3.8/8.2)

The key here is to take advantage of what you already know about respiration. There are many shared/neatly-contrasting features which connect the two processes. If your understanding of respiration is not yet what you want it to be, studying photosynthesis will be helpful in that respect as well.

Let's start out with a little silliness...

Chlorophyll is a pigment, with a characteristic common to many pigment molecules, alternating C-C double bonds, which make the molecule vulnerable to interaction with light...in the extreme, resulting in "photobleaching." (click on the pictures to enlarge)

Connecting to what was covered in 10th grade chemistry, light energy (here shown as a particle-like photon) interacts with the electrons in a lower energy orbital to excite them into a higher energy state. Chlorophyll molecules in the photosystems I and II become excited and excite the neighboring chlorophyll molecules in turn.

(left) As we saw in our demonstration with "spinach tea," if you illuminate a chlorophyll solution with a high energy UV light, the excess energy is given off as lower energy red fluorescence. (right) The graphs above show the correlation between light absorbed by chlorophyll (colored line) and the amount of photosynthetic activity that occurs of the plants are illuminated with any particular wavelength of light in the visible spectrum.

Now to basic business...light dependent reactions.

Nice, not-to-complicated, but not-too-simple, animation. Think about how the design reflects what is happening in the process. Click on the diagram to start.

And a clear diagram of the Calvin Cycle with "just enough" detail.

Each of these "steps" is truly a series of more complex reactions. The only change to note is that the IB preferred terminology for the product of carboxylation is "G3P" for glycerate-3-phosphate, instead of the term "phosphoglycerate."

How do we know the steps in the light independent reactions? A "lollipop" experiment...

Calvin and his team of scientists used a radioactive atom of carbon. By tracking this special carbon as it travelled through a plant, Calvin could map the process of how plants use carbon and water to create sugar.

Calvin did not use an actual plant. He used a tiny organism called a Chlorella. If you have ever been near the ocean and noticed that the surface of the water looks green, you are probably seeing exactly what Calvin saw-green algae. The single-celled algae was perfect for Calvin's experiment, because the process of photosynthesis is much faster in such a small organism. He filled a glass container with algae, and set up a bright light to enable photosynthesis. Then, Calvin followed the radioactive trail left as the algae made their food.(http://sophia.smith.edu/~dglass/history.html#)

Lollipop apparatus

Melvin Calvin, 1911-1997

Radioactive products made in chlorella, 5 seconds (top) and 30 seconds (below)

Fishing boat pulled over chlorella mat in China.

Chlorella as seen in light microscope

The remaining highlights of the unit include (1) the structure/function relationship between the structure of the chloroplast and the different sets of reactions that occur in each area, (2) the ways to measure photosynthetic rates [keep in mind as we head to a new student-designed lab] and (3) what factors are limiting as one looks at the dependence of photosynthesis rate on light intensity, substrate (carbon dioxide) concentration and temperature (be able to sketch these curves, with labelled axes). Refer to the slide show above for more information on this as needed.

Best check for understanding - can you compare photosynthesis and respiration? Can you identify useful contrasting features? Print this image and add your own additional notations.