Oxidative Phosphorylation

By the end of glycolysis and the Krebs Cycle, the glucose molecules are fully consumed. Carbon dioxide, 4 ATPs, 2 FADH, and 8 NADH have been produced. The reduced coenzymes (FADH and NADH) carry some electrons from glucose, and they are full of potential energy that need to extracted in order to recycle these molecules, and also to produce way more ATP. In this post we will see an general idea of what happens to these coenzymes and how different NADH is from FADH.

Coenzymes do not directly react with oxygen. The electrons carried by NADH are passed though different electron carriers until it reach the terminal electron receptor, oxygen. In fact, oxygen also picks up some water from the surrounding and forms water. Most of the electron carriers are embedded inside of the membrane (bacterias - cell membrane, and eukaryotes - mitochondrial membrane.)

The free energy resulted from this redox reactions is used in the phosphorylation of ADP. The overall process is known as "Oxidative Phosphorylation" or simply OxPhos.

Storing Energy in the Electrochemical Gradient

The potential energy acquired during the redox reactions of OxPhos must be stored temporarily before it is used to make ATP. This is accomplished by pumping hydrogen ions across the membrane (prokaryotes - plasma membrane, eukaryotes - mitochondrial membrane.) Enzymes that are responsible to catalyse the transfer of electron from one electron carrier to another (redox reactions) also helps to pump hydrogen ions across the membrane. Pumping of hydrogen requires active energy, because it is moving against its gradient in order to store potential energy in the electrochemical gradient.

Energy for pumping hydrogen ions

As we have previously seen, the process of transferring hydrogen atoms across membrane is a active process, but where does the energy comes from? It comes from secondary active transport. Thus, it acquires energy from other redox reactions that occur between electron carriers.

NADH transfer its electron to CoQ, which is a hydrophobic coenzyme that is located within the membrane. The enzyme the catalyses this redox reaction is known as Complex I. Now, CoQ in reduced form will transfer its electron to a hydrophilic enzyme called Cytochrome C, or only CytoC. The enzyme the catalyses this transfer is known as Complex III. Finally, CytoC transfers its electron to oxygen, through the help of Complex IV.

What about FADH?

The process of transfer of electrons from FADH to oxygen is very similar to the one regarding NADH. The difference however is associated with the use on enzyme Complex II. The use of this enzyme will NOT result in the pumping of hydrogen ions across the membrane, meaning that the oxidation of FADH will not pump as much hydrogen ion as of the one of NADH.

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.