Tag Archives: protein

The Molecule Of Life, Part II

Proteins are the molecules that are actively working during reactions. For example, in order for the electron transport chain (ETC) – the third stage of cellular respiration – to flow, a number of specific proteins must be present:

NADH and FADH2 carry the electrons to the protein complexes. Once there, ubiquinone and cytochrome C transport the electrons from complex to complex within the chain. At the end of the ETC, the ATP synthase enzyme is present, whereby it acts for the principal mechanism involved in the production of ATP.

This is one example amongst many. Although perhaps very obvious to all, it is worth reiterating here that respiration would not occur if it weren’t for the proteins involved.

MRS GREN is a way of remembering the seven processes an organism must consistently perform to count as being alive.

                                                         Movement

                                                         Respiration

                                                         Sensitivity

                                                         Growth

                                                         Reproduction

                                                         Excretion

                                                         Nutrition

If we were to look into each one of these processes we would see that, at the core, they all consist of protein activity. Along the same lines, would it be fair to say that the molecule that controls life is in fact the protein and not DNA? Although unconventional and perhaps heretic, it remains a just observation.

Continuing from the above, we know that the way in which proteins work relies on their movement. If a protein is left alone it does not move, so what causes the activity of proteins? It comes down to the signals that they receive and abide by. Well where do these signals come from? The answer, very simply, is the environment. Hold that thought.

The most important statement in biology is named the central dogma. It says that biology begins with DNA, which leads to RNA and finally to the proteins. However, what is ignored in this statement is that the DNA does not control itself. Genes are activated or deactivated as a result of the movement of regulatory proteins. The positioning of these DNA proteins is in turn controlled by environmental influences. So effectively, perhaps the central dogma should be revised to say the following:

Environment > Regulatory Proteins > DNA > RNA > Proteins

The above also erases a particular argument against the protein as the molecule that controls life. One might say that in order for the protein to be present and a reaction to be carried out, the protein must first be made by the DNA (example of a reference to the central dogma). However, to this I say the following: If part of a DNA strand needs to make a certain protein, it will be able to do so thanks to the movement of the regulatory proteins (see previous paragraph).

So where does this take us?

We have devalued the importance of the DNA as the molecule that controls life.

We have disproved the myth that the “brain” of the cell is the nucleus, and have concluded that it is in fact the cell surface membrane.

We have brought attention to the protein, and stated its crucial role in living processes and hence, in life.

We have considered the activation of the protein, as we know that when undisturbed, it remains latent.

We have reiterated that the protein is in action only when triggered by a signal.

We have considered the origin of these signals, which ultimately, is the environment. This not only encompasses messages transmitted by the brain, but also those put in place by the environment: the fields, messages and molecules that are always present around us.

These concepts spur questions that unfortunately cannot all be discussed in this article, but please do not hesitate to ask. I also strongly recommend that you look up Professor Bruce Lipton, whose knowledge, studies and thoughts are what led me to write this article. 

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The Molecule Of Life, Part I

Many people live under the false pretext that life on Earth comes down to the presence of the nucleus and its DNA. If we were to abide by this assumption, we would presume that an enucleate cell (lacking a nucleus) would not be able to function as it does normally. However, this is not the case. Experiments were performed whereby the nucleus of a cell was removed in order to see what would happen. The cell not only survived but also continued to carry out its normal living functions and processes. So the brain of the cell had to be present elsewhere.

Now consider humans. Without our brains we die. This leads us to question what it is exactly that the brain does to keep us alive. Well, it assesses our surroundings, taking in environmental information and transforming this data into signals that can be understood and acted upon in the body. It is also potent in its omission of some environmental signals as well as with the emission of messages sent by the body. Does the brain’s function sound familiar? Think back to GCSE biology, and the role of the cell membrane: “The cell membrane controls the movement of substances into and out of the cell”. So essentially, the human brain has the same role as the cell surface membrane.

This links back to one of my previous articles on the impact of genetics versus that of epigenetics. Naturally, the genetics of a cell comes from its DNA information in the nucleus. The influences of the environment, however, enter the cell via the cell surface membrane. Does that not validate the importance of epigenetics over that of genetics, now that we have established that the cellular brain is in fact the plasma membrane and not the nucleus?

Let’s now go back to the title – the molecule of life. What is it that triggers life processes to occur? And once the occurrence of a reaction has been triggered, what is it that enables the process to be carried out? Surely not the DNA as it does not leaves the nucleus, and we well know that reactions do not occur in the nucleus of the cell. Rather, they occur in the cytoplasm, where hundreds of proteins are present.

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RUBISCO (ribulose bisphosphate carboxylase/oxygenase)

Rubisco is a protein; the single most important enzyme known to man.

 Introduction

The carbon atom is found everywhere, as part of simple or complex structures. There are two carbon-containing forms that are most important to us, and particularly to Rubisco. The first is as an inorganic, highly oxidised compound found in air (eg. CO2). The second is found in the organic form, and referred to as an organic compound if it contains solely hydrogen and carbon atoms.

The carbon that makes up highly oxidised structures is difficult to get hold of and needs to be fixed in order to become of use. The process by which this occurs is called carbon fixation. Plants are responsible for fixing the carbon atoms into compounds rich in carbon/carbon double bonds and hydrogen atoms; they do this using energy from the sun.

Aim:

Rubisco has the important role of turning inorganic carbon – present in the air – into its organic forms.

(It is a bi-functional enzyme that catalyses the carboxylation and the oxygenation of ribulose biphosphate).

How:

Rubisco attaches the carbon atom (derived from CO2) to the ribulose biphosphate chain (a 5-carbon sugar). The addition of the extra carbon consequently lengthens the chains, which is in turn split by Rubisco in order to form two smaller identical ones. They each contain 3 carbon atoms and are known as phosphoglycerates.

93% of the time, the new sugar chain made (phosphoglycerate) is recycled and used to produce more ribulose biphosphate, as the carbon fixing cycle must be maintained. However every 6th molecule made is used either to make sucrose so that the plant can be fed, or to make starch for energy storage.

The Specificity of Rubisco:

The physiology and chemical properties of a diatomic oxygen molecule are very similar to that of a carbon dioxide molecule. The barely noticeable structural difference is that the size of an oxygen molecule is slightly smaller. This means that a carbon dioxide molecule will not be able to bind to a protein made complementary in shape to oxygen – such as haemoglobin – because it will not fit. However it does mean that an oxygen molecule can bind to an enzyme made specifically for carbon dioxide, and fit comfortably. This is unfortunately what happens with Rubisco and oxygen; the O2 will bind to the enzyme’s site designed for C02. This produces a faulty oxygenated molecule.

 

The Efficiency of Rubisco:

Rubisco works at a very slow pace. To give you some idea, whereas the average enzyme can produce 1000 molecules per second, Rubisco will fix 3 carbon atoms in the same time period.

Luckily, the plant can make up for this inefficiency by holding vast quantities of the Rubisco enzyme in the stroma of chloroplast organelles.

It is clear why Rubisco is the most common enzyme, as well as the most important one. Without Rubisco, the Calvin cycle (the metabolic pathway that is photosynthesis) could not begin and the level of carbon dioxide in the air would be ever increasing, and at a much higher rate than that caused by global warming.   

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