Fermentation and Biofuels

Economic and Environmental Impacts of Ethanol Biofuel Production From Plants

Biofuels have attracted a lot of interest as alternative sources of energy that are considered as more sustainable and "environmentally friendly." In fact, many nations around the world have heavily invested in biofuel production.

Nevertheless, several concerns have arose regarding the use of biofuels. One concern is regarding the amount of corn necessary to produce the ethanol required to replace the currently source of energy. The production of ethanol from corns also increases the eutrophication and pollution of groundwater and aquatic ecosystems. Leading to an increase in greenhouse gases, even though it is carbon dioxide neutral.

There are other types of plants other than corn that can produce biofuels as well. How do they do compared to corn?

Sugarcane

sugarcane produces ethanol in a way more efficient way than corns. Not only, it produces way more ethanol than corns, it actually doens't emit as much greenhouses gases as corns. Nevertheless, it does effect the environment once, in order to produce sugarcane fields, a lot of the rain forest must be cut down. Leading to a increase in impact on biodevisity and carbon dioxide emission to the atmosphere.

Wheat

Although Canada has a smaller biofuel industry than countries like USA and Brazil, we still have several plants that can be use in the production of ethanol. In West Canada, the plant of interest is wheat. The grain of wheat is rich in starch and it has been suggested that genetic engineering could further boost starch content is these grains, making wheat a very efficient source of biofuel.

The Biological Process of Ethanol Production From Fermentation of Plant Material

Bioethanol is produced when carbohydrates are fermented by yeast (a single-celled fungus). A very famous type of yeast is S. cervisiae, which has been used by humans for years to produce ethanol by fermentation.

The start point for ethanol production process is to provide the yeast with a source of carbohydrates, such as corn, sugarcane, and wheat. The yeast uses it as source of energy and carbon. It will break down simple sugars first (such as glucose) and it will generate ethanol and carbon dioxide.

Regulation of Enzymes

Allosteric Enzymes are a special type of enzymes that change their shape when bound with an activator or inhibitor. The change in shape changes the activation site, which effects on the efficiency of the enzyme. This is important in order to regulate the production of ATP depending on the present requirement of the cell.

Krebs Cycle

We have learnt previously about the pyruvate molecule, and how two of those are produced for every glucose molecule. Now we will see in a greater detail what happens after.

Fermentation

This is anaerobic process, meaning that no oxygen is required for it to happen. Fermentation can lead to lactic acid or ethanol and carbon dioxide + 2 ATP molecules. Some organisms are able to only live from fermentation.

We humans cannot live only through fermentation. This process is just temporary for us, only when oxygen is not available. NADH is not recycled because, even though during the process of fermentation NAD is back, when oxygen is once again available, lactic acid is transformed in pyruvate, and NAD transforms into NADH.

As well as glycolysis, fermentation occurs in the cytoplasm.

The Bridge Reaction

After glycolysis is done, and if there is oxygen available, then pyruvate is transported into the mitochondrial matrix and will reacted with coenzyme A, which will transform it into acetyl-CoA. The result also include the formation of carbon dioxide and 2 NADH (one for each pyruvate.)

This reaction is called the bridge reaction because it links glycolysis to the Krebs cycle (citric acid cycle).

The Krebs Cycle

The Krebs cycle is a series of 8 connected reactions. The first reaction includes the reaction of acetyl-CoA with oxaloacetate, interesting enough the eight reaction will form this reactant, hence the name "cycle"

Just like glycolysis we will cite the some wonders of this cycle:

1. It consists of 8 connected reaction, which some of them are even coupled reactions.
2. It is a cycle because one of the reactants of the first reaction is formed in the last reaction.
3. Every reaction is exergonic.
4. Every reactions has its own enzyme.
5. It forms 2 ATP molecules (1 per pyruvate)
6. It forms 6 NADH and 2 FADH for both pyruvates. Both have a lot of energy in their bonds.

The formation of NADH and FADH leads to this idea that they must be recycled. Therefore, it is important the presence of oxygen, because it allow for the oxidative phosphorylation to happen, which we will discuss in the next posts.

Glycolysis

After every meal we have, the food is broken down in our stomachs into small molecules. The most important molecule is known to be glucose. Glucose provides energy for all different kinds of cells and tissues in our body, allowing cellular processes to take place. This is done by the transfer of the potential energy found in the bonds of glucose into the chemical bonds of ATP, through biochemical reactions.

For the next posts, we will have a overlook in these biochemical reaction and their mechanism.

Glycolysis Overview

Glycolysis is a series of 10 connected reactions that will break down glucose and will result in pyruvate. The point of this post is not trying to get you to memorize, instead we will have a overview in some of the principles of this process, in order to comprehend it better.

The first thing to notice is that several molecules of ADP, ATP, NAD, and NADH are involved with the reactions. Glycolysis will result in the formation of two identical pyruvate molecules. Another thing to notice is that glycolysis is a anerobic process.

The 7 principles of Glycolysis

1. Glycolysis is a series of 10 connected reactions. Some of these reactions are coupled.
2. During the process of glycolysis, glucose is broken in half, hence its potential energy is rearranged in the bonds.
3. Every single reaction is exergonic (obviously). Some will small negative free energy, while others will have large.
4. Every reaction have its own enzyme. Interesting enough, cells can actually ihibit or activate them depending on how much ATP they need.
5. Glycolysis primes ATP. Which means that it actually uses 2 ATP molecules in order to make 4.
6. Glycolysis is anaerobic, but will produce two NADH molecules which will be used later on with their high potential energy levels.
7. It produces 2 pyruvate molecules, which are still full of energy and must be reused in another reaction.

What happens after glycolysis

We just talked about the formation of NADH. These molecules come from NAD, and these must me recycled, otherwise, there wouldn't be any more NAD to be used. 

Gladly there are several ways to recycle NADH. In order to do so, there must be a oxidizing agent, which can be oxygen (if present), or pyruvate itself. When pyruvate is used, it can either format lactic acid, or ethanol and carbon dioxide.

When the presence of oxygen occurs we will have what we called Oxidative Phosphorylation which we will see in later posts.

Membrane and Transport

The cellular membranes are there to isolate the cell from the outside environment. Nevertheless, cells are under constant conditions such as:

1. Cells live in dynamic environments, where conditions are constantly fluctuating;
2. Cells must maintain homoeostasis;
3. Cells must regulate the concentration of molecules inside them;
4. Cells must regulate the transport of molecules across membranes;

Therefore, cells must have a selective barrier.

This selectiveness is due to the very selective permeability of the phospholipid bilayer. It allows small uncharged molecules, small hydrophobic molecules to pass freely, but won't let any charged or large molecules to go through easily.

There are two main type of transport across cellular membranes: (1) diffusion and (2) active transport.

1. Diffusion is also known as passive transport. It does not require any source of energy because the molecules are moving down in their concentration gradient (high to low). It is divided into two types: simple diffusion and facilitated transport.
2. Active transport requires energy because the molecules are being transported against its concentration gradient. The source of energy comes from a reaction or process that is coupled with the transport so that there is a negative free energy overall, and therefore, is spontaneous.It is divided into primary transport and secondary transport.

Simple Diffusion

Occurs when molecules are able to pass through the membrane with no help from the any protein. Oone example would be the transportaion of oxygen. Oxygen is not polar or charged, so therefore can pass through. It is also found in greater quantities outside the cell, then inside of it. The membrane also lets the passage of water and carbon dioxide pass thorough, even though they are polar, but they are also very small.

Facilitated Diffusion

The diffusion of some molecules, as sodium ions requires a protein to facilitate the process. This is because these molecule can be charged or too big. Therefore they will need proteins to work as gates so they can pass through the hydrophobic membrane.

Water can also be transported through facilitated transport. Aquaporins are water channels that increase the rate of water movement!

Primary Active Transport

Some molecules don't have the chance to be pass through by passive transportantion, simply because they are already found in higher concetration inside the cell (or outside if the cell is trying to exit it).  Nevertheless, these molecules will need energy in order to be transported. In primary active transport the enrgy comes from other reactions such as the hydrolysis of ATP(so it basecally says that PAT uses ATP).

Secondary Active Transport

This mode of transport acquires energy from other transportation process, which must be passive since it provides energy for the other type.
There are two types: Symport (when the two transportations are in the same direction) and antiport (when both are going in opposite directions.)

Energy at Membranes

Cells need to isolate their molecules, organelles and processes that are occurring within them. That is why, cells have thin membranes that surround it. These membranes are not only use to separate compartments, they play a very important role in energy processing.

Cells have the tendency to separate a high energy outside from a lower energy inside. This is done by the difference in electrical charges associated with certain ions and differences in the concentration of certain molecules.

A good example of these difference would be the hydrogen ion. They are usually found in greater amounts on the outside of the cell. Therefore, there is a greater positive charge outside than inside.  This difference in charges and concentration will cause the hydrogen ions to push themselves into the cell. Now, this process is very important because it does generate ATP, once it passes by a "turbine" within the membrane, generating a useful work.The sum of the concentration push and electrical push is known to be electrochemical gradient.

The cellular membrane is formed primarily by phospholipids, these make the main structure of this membrane in what is called bilayer. These phospholipids are divided into two parts: The head group which is hydrophilic, formed by several oxygen atoms and one or more nitrogen atoms (polar bonds). The head group likes to interact with water via dipole-dipole interactions, hydrogen bonds, and even ion-dipole interactions.  This allows the build up of sterols, which will provide the membrane rigidity and integrity during temperature changes.


The second part of the phospholipids stay in the centre of the membrane. They do not contain any oxygen nor nitrogen atoms, thus, they are hydrophobic, and will have hydrophobic interactions with each other. There are two type in the hydrophobic portion: (1)saturated and (2)unsaturated portions.

1. Saturated layer are packed more tightly and make the membrane less fluid
2. Unsaturated layer are less packed and make the membrane less packed, making it more fluid.

Membranes keep a constant state of flux on its membrane between these two forms, so homoeostasis can be achieved.

This hydrophobic portion of the membrane will keep H ions out or in, creating a electrochemical gradient.  That is why there will be proteins built into the membrane. These proteins will not only work as gates for this chemical to pass through the membrane, but they will also play a very important role in production of energy and sensory information.

Membranes keep a constant state of flux, so homoeostasis can be constantly achieved regardless of change in environment.

Summary: The basic structure a cellular membrane is demonstrated by the the Fluid Mosaic Model, which consists of a lipid bilayer which has a hydrophobic centre and hydrophilic surfaces. proteins may be attached to the surface of the lipid bilayer or inserted into or across it. Besides providing physical separation cellular membranes are very important for energy processes in the cell. If the concentration gradient is formed which stores free energy. If the number of cation or anions on one side of the membrane is greater than the number of counter-ions, then an electrical gradient is also formed which stores free energy. Often the two together to form an electrochemical gradient.

Classification of Organisms

In order to comprehend a little better the vast diversity of organisms in nature, we have looked for classifications systems. Traditionally, animals have been classified based on the morphology (shape and structure, or simply "how they look like"). This led to the creation of the 5 kingdoms. Nevertheless, a better and more accurate system of classification is used today. Now, organisms are based on their:

1. Phylogenetics;
2. Cellular complexity;
3. Energy Source;
4. Carbon Source.

Classification based on phylogenetics

Phylogenetics is just a fancy word for molecular information, specifically ribosomal RNA gene sequence. Interesting enough, each organism has a specific sequence. Therefore, by comparing the sequence of genes in different organism we can see how similar they are from each other. This led us to assume that all organisms could be grouped into three different domains: (1) eukaryota, (2) bacteria, and (3) archaea.

1. Eukaryota include organisms that are relative complex compared to their other domains. They have bigger and more complex cells and membrane bound organelles also.
2. Bacteria are found in several forms and shapes. These are single-celled organisms that have a great diversity on ways to metabolise energy. Bacteria also do not have membrane bound organelles like eukaryota organisms.
3. Archae organisms are very similar to bacteria, so similar that they were once formerly considered to be bacteria! Nevertheless, by comparing rRNA, it was concluded that they belonged to different domains. These organism have very usual shapes, and live in very extreme environments, such as high salt concentration, acidic water, or thermal hot springs.

A weird fact is that the organisms from the domain archae, in phylogenetic terms, is more similar to the organism in Eukaryota than it is to the ones in bacteria. This can only suggest that these two similar domains have been diverged from a common ancestors.

Classification based on cellular complexity:

When classifying animals, we must analyse in detail the complexity within the organism. Therefore, we will divide the organisms based on the complexity of their cells. This leads us to two types of cell: (1) Prokaryotic, and (2) Eukaryotes.

1. Prokaryotic cells are small and simple when comparing to eukaryotes, therefore, having a higher surface-to-volume ratio. The do not have membrane bound molecules, and its genetic information is all around the place within the cell. By being small though, prokaryotic cells don't need much in order to maintain themselves.
2. Eukaryotic cells are way bigger and more complex. They do have membrane bound molecules, and their genetic material are located in a membrane bounded nucleus. These membrane bound molecules are very important because they allow specific compartments to carry out specific function like energy production. This allows this big cells to maintain themselves.

There are two very important misleading ideas in this topic:

- The first one is regarding the uni-cellular organisms. These are not necessarily bacteria or archea. Some are considered to be eukaryota.
- The second one is the prokaryotic organisms are not always similar to each other, we have already seem that archea is very similar to eukaryota and not to bacteria.

Interesting enough, we can think about relationships between prokaryotes and eukaryotes. Think about your mouth, there are billions of prokaryotes organisms living there, in a symbiotic relationship.

There is a theory called endosymbiotic theory. It suggests that some organelles in eukaryotic cells such as mitcochondria and chloroplasts were originated from prokaryotes! And there is some evidence for this statement: There are many symbiotic and endosymbiotic association today, these organelles have their own DNA and divid by binary fission (just like prokaryotes), and their ribossomes are more similar to prokaryotes than to eukaryotes.

Classification based on energy and carbon source

Organisms that acquire the energy from the sun are said to me phototroph, other organisms which have their energy coming from the chemical bonds of molecules are said to be chemotroph. We also know that there are two types of chemotrophs: those who get energy from organic chemical compounds (chemoorganotrophs), and those who get energy from non-organic chemical compounds (chemolithotrophs).
Now we will learn that the source of carbon can actually influence on the classification of organisms.
Those organisms that have their carbon source from carbon dioxide are said to be autotrophs, and those who get from organic compounds are said to be heterotroph. When naming, we put both energy and carbon source names into one.
For example, plants are said to be photo-auto-trophs, because they get their energy from the sun and the carbon dioxide is their source of carbon. Us, humans we are chemo-organo-hetero-trophs. Can you say why?

Summary: Phylogenetic classification of organisms based on rRNA sequences has led to classification into theree domains in life - bacteria, archae, and eukaryota. Although archae are prokaryotic cells, they are more closely genetically  related to eukaryote than bacteria as is shown by the examples in the text.  The classification of organisms based on energy source (photo- or chemo-) and carbon source (auto- or hetero-) lead to six different classes.