Tag Archives: metabolism

All in a kerfuffle

I’m all bent out of sorts since I decided to write about the green coffee extract paper popularized by Dr. Oz. 

Here’s the problem: in my last post I attempted to unpack the data presented in the article describing a weight loss trial using this supplement. Yet, the closer I examined the data, the more clear it was to me that the data presented in that paper does not support any conclusions.

This does not mean that the supplement is effective or not. It doesn’t even mean that the group is lacking in data that would answer the question. It merely means that the numbers they present and the descriptions of their methods do not allow one to scrutinize the data in a way that supports or refutes their claims.

ImageFor anyone interested in a fun discussion of statistics and what they mean, I strongly recommend the classic text, How to Lie with Statistics, by Darrell Huff.It’s a bit out of date, but still a lot of fun to read and educational for those who have not spent much time analyzing figures.

One thing the Mr. Huff’s book does well is brings the reader into the discussion of data and how to present it. A lot of his focus is on how advertisers manipulate their graphs and language in order to obfuscate the truth.

I don’t think this coffee extract paper is intentionally obfuscating the truth, rather, I think the confusion comes from an inability of the authors to present their data clearly (even to themselves perhaps). I’ve worked in a number of labs with a number of scientists in my life and I can say with conviction that not all scientists ability to analyze their data is the equal. In fact, I have seen a number of presentations where the presenter clearly did not understand the results of their own experiments. I can say that sometimes I have not understood my own data until presenting it before others allowed us to analyze it together (i.e. I am not exempt from this error).

I would love to have the opportunity to examine the raw data from these experiments to determine if they really do address the question – and whether, once addressed, the question is answered. I’m going to appeal to both the journal and the authors for more clarification on this and will report my findings here. 


Leave a comment

Posted by on July 23, 2013 in Uncategorized


Tags: , , , , , , , , , , ,

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).





Leave a comment

Posted by on October 9, 2012 in Uncategorized


Tags: , , , , , , , , ,

Cellular Respiration

Photosynthesis is the process of capturing energy from the sun and converting it into a chemical form that can be stored (as glucose) for harvested at a later time.

            solar energy + H20 + CO2 –> glucose + O2

Cellular respiration is the action of harvesting that energy and converting it into a form usable to power cellular processes.

            glucose + O2 —-> H20 + CO2 + ATP

If solar energy and ATP are equated with simply ‘energy’ , then these two reactions are the same, only in opposite directions.

Cellular respiration begins in the cytoplasm, where the reaction occurs regardless of whether O2 is present or not. This first stage, glycolysis (from sugar + breaking) produces a Net of 2 ATP as well as the electron carrier molecules, NADH. If there is no Oxygen present (Anaerobic conditions), then this is the only energy-producing step that can occur and fermentation occurs in order to regenerate the NAD+ required to continue gylcolysis.

If O2 is preset (and if we are talking about eukaryotic organisms) then the products of glycolysis (two pyruvate molecules) will be transported into the mitochondrion for further processing. In this space, pyruvate is converted into AcetylCoA, which subsequently enters the Krebs / Citric Acid Cycle. No substrate survives beyond this point. There is a small amount of ATP formed by substrate level phosphorylation, but high energy electrons in the form of NADH and FADH are passed to the Electron Transport Chain.

The Electron Transport Chain is the last step of cell respiration and occurs when a high energy electron is passed into the chain, the electron is passed from one member to the next drawing H+ ions from the Matrix into the inter membrane space. As H+ ions accumulate in the intermembrane space both chemical and electrical concentration gradients. When this gradient is released and H+ ions are allowed to pass through specialized enzyme / channel proteins, the energy is harvested to form ATP via the process of oxidative phosphorylation / chemiosmosis.


I will attach a diagram of this series of reactions tomorrow and perhaps add some additional materials. Right now, I’ve already fallen asleep three times just in typing this.



Leave a comment

Posted by on October 8, 2012 in Uncategorized


Tags: , , , , ,

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:

Leave a comment

Posted by on September 17, 2012 in Uncategorized


Tags: , , , , , , ,