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A simple graphic representation of Cellular Respiration

Here are the several steps of Cellular respiration summarized in a flow chart. I suppose I could have used true flow chart symbols to represent each step and then a decision diamond just after the glycolysis reaction to ask whether oxygen was present (and the aerobic reactions could follow) or absent (leading to fermentation).

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Posted by on October 9, 2012 in Uncategorized

 

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Intro Biology – Photosynthesis

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A note on the order of my lectures:

So far we have discussed the cell itself and divided its several functions amongst organelles that carry them out. We have also discussed the properties of membranes and how diffusion operates across them as a passive event. As a consequence diffusion can be opposed, but requires energy input. Lastly, we covered energy and how it may be converted into various forms or used to do work. Within the cell this work is often guided by enzymes.

 

Where we are going:

In the next section we will address how energy is captured by living things from the environment and converted into a form that may be stored. In the chapter after that, we will consider how this captured energy can be brought out of storage and converted into a useful form for enzymes to use in getting specific jobs done.

 

Photosynthesis

 

As stated above, the purpose of photosynthesis is to convert energy from the environment (solar energy) into a new chemical form (glucose) that can be stored for later use by cells.  The process of photosynthesis is completed, in eukaryotic cells, entirely within organelles called chloroplasts. These are organelles that are theoretically descended from prokaryotic cells that engaged in symbiotic relationships with larger cells but are now inseparable parts of the larger cells. As such, we recognize that there are other cells that can carry out photosynthesis, but we will restrict our discussion to that carried out in plant cells.

 

The basic reaction occurs in two phases, the light reactions and the dark reactions. Despite their names, both occur at the same time, typically when it is light.

 

The light reactions are when photons from the sun transmit energy into pigment molecules in the chloroplast. From there, electrons carry the energy from one  molecule to the next in an electron transport chain that functions to pump protons (H+) across the membrane. In this way an electrochemical-, or proton-, gradient is established.  This gradient is a form of potential energy that can be released when protons diffuse back across the membrane passively, through ATP synthase proteins that form channels through the membrane. When H+ ions pass through this channel energy is captured to synthesize ATP through a process called chemiosmosis. This is very analogous to the way that dams capture the energy of water passing through. The high energy electron is finally passed off to form NADPH, a high energy electron shuttle. Because the reaction cannot repeat until the electron is replaced in the photosystem, one is taken from H2O, which splits to form O2 and more H+ ions. The end result of the light reactions is the formation of ATP and NADPH (and O2 as a waste product) from solar energy and H2O.

 

This summary does not include details reactions starting from Photosystems I and II specifically. Nor does it include the cyclic reaction.

 

The dark reactions will be covered in our next class a little more extensively, but basically, their function is to use the ATP and NADPH produced in the light reactions as power to synthesize glucose from CO2.

 

 

 

 
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Posted by on September 26, 2012 in Uncategorized

 

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How Do Enzymes Lower the Activation Energy?

In class today we discussed three mechanisms for how enzymes function. These three mechanisms are:

1. Bringing substrates together in a way that promotes the appropriate interaction.

2. Another way they function is to couple exergonic and endergonic reactions.

3. They also lower the Activation Energy of the reactions they catalyze

 

Ashley asked a good followup question: how, exactly, do enzymes lower the activation energy in reactions?

I’ve looked around for a good explanation of this without finding much satisfaction. One explanation found on Wiki.answers was that, according to the induced fit model, when substrates bind to enzymes, there is strain put on the molecule that promotes the reaction. But this answer felt unsatisfactory for a couple reasons: First, it was unsupported by any links to primary data and second, it’s really only a partial answer – i.e., does it take energy to get the enzyme into this strained conformation? If so, where does that energy come from (perhaps the particle’s movement?) If it doesn’t require energy, why do the substrates get themselves into this position?

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Enzyme placing strain on substrate

A better answer was found from Science magazine back in 2004. The article, Mireia Garcia-Viloca, Jiali Cao, Martin Karplus, Donald G. Truhlar. “How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations.”Science303:186 – 195 (9 January 2004), refers back to a statement by Linus Pauling where he posited that the only actual power enzymes have is in stabilizing a transition state. What does this mean? It means essentially the same thing as was stated above – however it also refers to a kind of ‘in between’ state that substrates enter while bound to the enzymes that makes it easy to convert into the ‘desired’ product.

Apparently, people have observed this lowering of the activation energy, but it’s been difficult for even those who study these things to define. I’ve posted the article on blackboard if any of you are interested in taking a peak at it.

 

 
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Posted by on September 20, 2012 in Uncategorized

 

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This week in General Biology

First Law of thermodynamics in action – Image courtesy of McGraw Hill

This is the first fun week in my biology class. (Fun for me) We’re starting to talk about energy and how it is handled and used by living organisms. As usual, my class is focused on animal cells as my standard model, but this all applies to any cell really.

The big topics of the week are to understand the nature of energy through the lens of the first (and second) law of thermodynamics. It’s the one that says, ‘Energy cannot be created or destroyed, only converted from one form to another’. The second law adds on a statement about entropy and how all energy conversions are less than perfect. The result is loss of energy – typically in the form of heat.

So, energy can’t be created or destroyed, fine. What does it matter to us?

It matters because (to paraphrase the author of our textbook, Mader):  Life itself is but a temporary condition purchased at the cost of a continuous expenditure of energy.

“Well, in our country,” said Alice, still panting a little, “you’d generally get to somewhere else — if you run very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

-Lewis Carol

We haven’t talked about where the energy comes from (specifically) but we do know that plants and other autotrophs convert solar energy into chemical energy that can be stored as sugar. However, when that energy is required to get something done it must be converted into a more useful form: ATP.

ATP is the coin of the cellular realm. Prokaryotes and Eukaryotes alike use ATP to power their enzymes. Enzymes are molecules that do cellular work, whether it be moving substances across a membrane, building complex molecules, replicate DNA or any of the many other functions of the cell. Enzymes do the work, ATP supplies the power.

Enzymes take reactants and combine them or break them to form products. This reaction happens where the reactants bind in the active site of enzymes.

We will also be looking at how enzymes are regulated within (or outside of) the cell. It wouldn’t do to have enzymes active all the time. What if a digestive enzyme became active as soon as it was made? It could damage the cell that made it. What is DNA polymerase was active all the time (we haven’t discussed this enzyme in class yet, but it copies DNA)? Random extra copies of DNA would not be useful.

Instead, enzyme activity is governed by two major types or regulators:

1. Competitive Regulators

2. Non-Competitive Regulators (There are also non-competitive activators as well)

No one enzyme does it all alone though. Instead, there are many, many enzymes that each have very specific jobs to do. These operate in conceptual pathways made up of strings of enzymes each doing one part of the work along the way. These pathways are referred to as metabolic pathways and may build (anabolic) or break down (catabolic) other molecules.

A last for of enzyme regulation involves the end product of a series of reactions going back and acting as an inhibitor to an early stage of the process. This is known as feedback inhibition and can be a very valuable way to save energy.

I hope that acts as enough of a primer for class this week because I’m getting tired and starting to find myself staring at the screen here in front of me for long moments. Here’s a trippy clip from the 1985 TV adaptation of Through the Looking Glass with Carol Channing and Ann Jillian:

 
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Posted by on September 17, 2012 in Uncategorized

 

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Intro Bio -Day 1

The first class of Intro Biology was yesterday and perhaps I was a bit too … familiar.

I’ve been teaching this class for a number of semesters now and my preparation time has gone down to a minimum – not to say that I don’t prepare, in fact, I prepare quite a lot. That said, I think more about what major concepts I want to get across during a class and don’t worry as much about the small stuff. Because the first day doesn’t have that much to it anyway, I know I could have structured my day a little better.

Instead, I may have come on fairly strong – piping at full steam under the power of a towering cup of cafe americano.

Here’s the structure of Day 1:

Sign in, pick up packets and go through the syllabus.

I also spend some time showing off the iBook I put together as a student handbook and explain how these will all be available as interactive software on the school’s iPads (oooohhh. – I think I was the only one impressed)

That is biology?  – The study of life.

What is it to be alive? – Harder to put into words than you would guess.

But it can be estimated by a series of characteristics and something called Cell Theory.

And Cell Theory, by the way, is one of the central concepts of biology.

What are the others?

Germ theory – some micro-organisms cause some diseases (a direct derivative of cell theory) Can be demonstrated by following Koch’s Postulates. Discuss some examples and then shelf – Germ Theory is the focus of my entire microbiology class, we don’t discuss it much in general bio after the first couple days.

The Central Dogma – DNA –> RNA –> Protein

Information –> molecules that carry out work

Inheritance and Evolution – How is information passed from one generation to the next. How do the mechanics of this work and what does that demonstrate about the history of life.

Follow up with how science is actually nothing but a systematized way of asking questions of nature  – play an excerpt from the Mischel’s Marshmallow’s episode of the RadioLab podcast (http://www.radiolab.org/blogs/radiolab-blog/2009/mar/09/mischels-marshmallows/). I cut off right after Jonah Lehrer cuts in saying that the difference in SAT scores is 200 pts+ for kids who can exhibit self control at an early age. Then we talk about what the question was, what the data was, how it was interpreted and what subsequent hypotheses can be suggested.

Actually, it all sounds quite reasonable here, but I might have just presented it a bit too frenetically. I actually get so excited about teaching that I have trouble containing myself. Especially after a whole summer of having no ‘audience’ – I need my stage-time!

So that was day 1. I’m only teaching one section this semester and I’m realizing that it’s not enough! Damn. They offered me more and I refused it. Ughhh. Well, the life of an adjunct. If they’d offer me a fulltime position it would be different.

An aside:  There is a part of me that agrees with my former mentor’s philosophy that if you come down on them and make the class a challenge right out of the gate, then you never have to deal with the chaff at all and you get nothing but the best students coming back.

There’s another part of me that thinks (perhaps unjustly) that, “yes -but you’re teaching ivy league students taking advanced immunology. I’m teaching a intro biology to a jr. college class.”

 
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Posted by on August 22, 2012 in Uncategorized

 

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Ideal Gas Law

Many years ago, as a grad student in Philadelphia, I used to tutor Biology and Chemistry in the evenings. This was my first introduction to working directly with students and I found it to be challenging, educational and quite fulfilling (and it also paid pretty well too). Although I consider myself a Biologist, I might have actually had the most fun tutoring Chemistry. This was mostly because chemistry is really just a couple of relatively simple equations that explain some neat stuff about the world.

Because the equations are fairly simple, the greatest challenge was to keep it interesting enough to be worth practicing. My solution to this was to adapt some Greek mythology to include questions about chemistry. Ever since then, I have wanted to elaborate on this idea and write it up in a way that others can use my examples to learn about science. So, perhaps seven years later I finally decided to just do it. Last night I began work on my retelling and have gotten fairly far along. I have an idea that it would make a fun animated book and I think the iBook authoring tool might just make it a snap to put together into something professional.

Now, I just need to contact some artists to work on the illustrations I want to put into it and finish writing out the text. I think I got about 1/3 of the way through the meat of the matter last night. Unfortunately, this situation reminds me a lot of the central problem of DownHouse Software, i.e. I can write the ideas out and maybe even set a decent design in place, but I don’t have the skills to create the artwork required. I’m ever in need of a collaborator… well, really a team of collaborators, to make my ideas come alive.

Perhaps this is a good project for Kickstarter?? I always wonder about using a product like that. Can I put enough of my creation out there that people will recognize the value without getting into a position of being scooped – because the whole problem is that I need others to make it happen. Maybe I’m just paranoid. But you would be guarded too if you didn’t have much else going for you professionally.

 

OK, enough blabbing. I want to finish my outline, flesh it out with some dialog and contact an illustrator or two. 

 

 
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Posted by on August 1, 2012 in Uncategorized

 

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