Electron transport chain

The electron transport chain (ETC) takes place in the inner mitochondrial membrane. During this process, the electrons donated by the electron carriers (such as NADH) pass through a chain of protein complexes embedded in the inner mitochondrial membrane. These electron carrieres were reduced during processes occuring before the ETC, for instance glycolysis and citric acid cycle.

(the ETC takes place in the inner membrane)

The movement of electrons initiates pumping of protons to the intermembrane space. This way, a proton gradient is created, and thus, the protons from the intermembrane space will flow back to the matrix through the ATP synthase, which is embedded in the inner mitochondrial membrane. When protons flow through the ATP synthase, ATP is made. 

The image above gives us a pretty detailed picture of the process. Let's now examine it:
As you can see, there are four protein complexes embedded in the inner mitochondrial membrane. The ATP synthase, which you can see on the right side of the image, isn't considered a part of the ETC. Let's look what happens in each complex:

(PLEASE LOOK AT THE PICTURE ABOVE FOR REFERENCE. I ALSO INVITE YOU TO WATCH MY VIDEO ABOUT THIS TOPIC HERE)

Complex I: The NADH donates its two electrons to complex I. These electrons are first accepted by FMN, and then flow to the iron-sulfur center, which is also an electron acceptor. Next, these two electrons are transferred to a mobile protein called ubiquinone (or coenzyme Q). Coenzyme Q then moves through the phospolipid bilayer and donates these two electrons to complex III (yes, to complex III, not to complex II). This leads to pumping of four protons (4 H+) to the intermembrane space.

But let's hold on for a second and see what happens in complex II:

Complex II: This is where succinate comes in and reduces FAD to form FADH2. This way, it donates two electrons. These two electrons are going to be transferred to the iron-sulfur center and later to ubiquinone. 

Complex III: The ubiquinone reduces the cytochrome b by giving away the two electrons. Then, cytochrome b is oxidized and the electrons travel to the iron-sulfur center. From there, they are passed to the cytochrome c1. Next, the cytochrome c1 captures these two electrons. Since cytochrome c1 can move from complex III to complex IV, it moves and thus carries these electrons to complex IV. When electrons are transferred from complex III to cytochrome c, four protons are also pumped from the matrix to the intermembrane space.

Complex IV: First of all, after cytochrome c has arrived, it gives the two electrons that it carries. These electrons are given to reduce cytochrome a. Then, they are passed to cytochrome a3, and later, to oxygen, the final electron acceptor. When oxygen accepts electrons (and two protons from the matrix), water is formed. When the electrons are transferred in complex IV, only two protons are pumped into the intermembrane space.

ATP synthesis:
(the awesome picture below, which I found online, for educational purposes only, illustrates the process)

The movement of electrons provided energy for pumping protons to the intermembrane space. Next, these protons are going to flow through the ATP synthase back to the matrix. As they flow through ATP synthase, they initiate movement of the top part of the ATP synthase (the one with C10 subunits). This again makes the gamma subunit spin. Since the lowest part of the ATP synthase doesn't move, the spinning of gamma subunits causes conformational changes in the beta subunits. These beta subunits are the subunits that synthesize ATP out of ADP and Pi, which are already present in the matrix.

Citric acid cycle

(PLEASE CHECK OUT THE VIDEO ABOUT THIS TOPIC :))

The citric acid cycle is the process that occurs during cellular respiration after the cell has successfully completed glycolysis and after the pyruvate has gone through the pyruvate dehydrogenase complex, where the end product was the Acetyl-CoA. This molecule is now going to be oxidized to CO2, by the series of reactions in the citric acid cycle. During the citric acid cycle, the cell makes some ATP, GTP and some electron carriers: NADH and FADH2. These electron carriers are later going to be utilized in the electron transport chain, to make more energy. The citric acid cycle takes place in the mitochondrial matrix.

The steps of the citric acid cycle:

1. Oxaloacetate is joined together with Acetyl-CoA, forming citrate. One water molecule is consumed, and the CoA is kicked off. The enzyme that is used here to catalyze the reaction is called citrate synthase.

2.  Citrate is isomerized to form isocitrate. The enzyme that catalyzes this reaction is called aconitase.

3. Isocitrate is oxidized to form alpha-ketoglutarate. During this reaction, an NAD+ is reduced to form NADH, and carbondioxide is also released. The enzyme that plays the crucial role here is the isocitrate dehydrogenase

 4. Thanks to the alphaketoglutarate dehydrogenase, the alpha-ketoglutarate becomes succinyl CoA. An NAD+ gets reduced and forms NADH, the CoA is joined to the molecule and CO2 is released.

5. Succinyl-CoA is now converted to succinate. The CoA is kicked off, and one GDP gets reduced to form GTP. An ADP comes in and takes the phosphate group from the GTP, so that it can become ATP. The enzyme that catalyzes this reaction is called succinyl-CoA synthetase. It has this name because the reaction is reversable.

6. The succinate is oxidized into fumarate. Two of the hydrogen atoms in the succinate are kicked off and picked up by the FAD. This way, the FAD is reduced to form FADH2, which is later going to be utilized in the electron transport chain. The enzyme that removes these hydrogens from th succinate is called succinate dehydrogenase.

7. Fumarase reduces fumarate to form malate. The way it does that is that it joins one water molecule to the fumarate.

8. Lastly, malate dehydrogenase removes hydrogens from the malate. Thus, malate is converted back to oxaloacetate, the molecule we started with. The hydrogens are picked up by the electron carriers.

Pyruvate dehydrogenase complex

Pyruvate dehydrogenase complex is a mechanism that occurs between glycolysis and the citric acid cycle. This is because pyruvate cannot enter the citric acid cycle right after glycolysis. The purpose of pyruvate dehydrogenase complex is to modify (or convert) pyruvate, the end product of glycolysis, to the acetyl CoA, which enters the citric acid cycle.

The enzymes involved are:

• E1: Pyruvate dehydrogenase (the TPP, or thiamine pyrophosphate is attached to it)
• E 2: Dihydrolipoyl transacetylase (the lipoic acid is attached to it)
• E 3: Dihydrolipoyl dehydrogenase (the FAD is attached to it)

Let's now look at what happens in details (please, look at the picture below while you read):

 E1:

First of all, pyruvate comes in and interacts with TPP, which is attached to E1 (pyruvate dehydrogenase). TPP has a ring that interacts directly with pyruvate. As a result, a CO2 is released, and the rest of the pyruvate (the hydroxyethyl group) is attached to the TPP, forming hydroxyethyl TPP.

E2:

Next, the hydroxyethyl group is transferred to the disulfide bond in the lipoic acid. Remember, the lipoic acid is attached to the second enzyme (E2) of the pyruvate dehydrogenase complex, the dihydrolipoyl transacetylase. That leads to the reduction of one of the sulfurs, because it gains hydrogen (this hydrogen comes from the hydroxyethyl group). The hydroxyethyl group without one of this hydrogens, which was given off to this sulfur is now forming acetyl group. An acetyl group attached to a sulfur forms a thioester bond, which is a high energy bond. The CoA-SH comes in and takes the acetyl group from this sulfur on the lipoic acid. CoA-SH also gives of its hydrogen to the sulfur, so now, we have made the acetyl CoA.

(Both of the sulfurs that before formed the disulfide bond are now reduced, because each of them has a hydrogen)

E3:

Furthermore, the lipoic acid cannot react with the hydroxyethyl TPP, because it doesn't have the disulfide bond. The FAD, which is attached to the third enzyme, dihydrolipoyl dehydrogenase, picks up these hydrogens, regegenerating the disulfide bond. As a result, FADH2 is formed. However, it cannot flow right to the ETC (electron transport chain), because it is attached to the dihydrolipoyl dehydrogenase. The NAD+ then comes in and becomes reduced to NADH + H+.

In addition:

The TPP is regenerated when hydroxyethyl group is removed from hydroxyethyl TPP.
The lipoic acid is regenerated when the disulfide bond is regenerated.
The FAD is regenerated when NAD+ comes in and picks up the hydrogen (a hydrogen ion is also released as a result of that) from FADH2.

This is going to be much easier to understand if you watch my video about this :).

Enzymes

Please, check out my video about enzymes :)

What are enzymes?

Enzymes refer to proteins that catalyze chemical reactions in our body. They are also called catalytic proteins. Enzymes speed up (or catalyze) chemical reactions by lowering the energy of activation (EA), which is the amount of energy needed to start a reaction. Enzymes exhibit tertiary structure.

How do enzymes work?

An enzyme binds to a substrate, forming enzyme-substrate complex. Thus, enzymes bind to the substrates when they are ''in action'', or when they catalyze a reaction. When an enzyme binds to a substrate, the shape of the enzymes alters as the substrate enters the active site, which is the place on the enzyme where the substrate can bind. Enzymes are substrate specific, which means that for instance enzyme A binds only to the substrate A etc.

However, enzymes often require assistance from substances called coenzymes and cofactors. These are substances that help enzymes in reaction catalysis, but cannot catalyze a reaction on their own. Coenzymes are organic substances, while cofactors are inorganic.

Competitive and noncompetitive (allosteric) inhibition

The enzymatic activity is highly controlled and regulated. This can be done in a number of ways. For instance, genes that code for a specific enzymes can be switched on and off. The enzymes that have already been produced are regulated by competitive and noncompetitive inhibition.

Competitive inhibition means that the substrate and a substrate-like substance (an inhibitor) ''competete'' for the active site of the enzyme. If the inhibitor binds to the enzyme, the enzyme won't work.

Noncompetitive inhibition, also known as allosteric inhibition, means that the inhibitor binds to another site of the enzyme (not to the active site). That causes the whole enzyme to undergo a change in its conformation, and the active site is changed. Thus, it's impossible for the substrate to bind to the enzyme. 

The steps of glycolysis

PLEASE WATCH THIS VIDEO THAT I'VE MADE ABOUT GLYCOLYSIS :)

Step 1:

A phosphate is attached to the glucose molecule. The phosphate comes from ATP, which becomes ADP after donating the phosphate. The enzyme that facilitates this reaction is called hexokinase. When the first step is finished, we have
glucose-6-phosphate.

Step 2:

An isomer of glucose-6-phosphate is created by the enzyme phosphoglucose isomerase. The isomer created is called fructose-6-phosphate.

Step 3:

The enzyme called phosphofructokinase attaches a phosphate from ATP to fructose-6-phosphate. The phosphate is attached on the first carbon of
fructose-6-phosphate, so the product that is formed is fructose1,6-bisphosphate. Of course, ATP donated a phosphate, so it left off as ADP.

Steps 4 and 5:

In the fourth step, the enzyme aldolase splits fructose 1,6-bisphosphate to two three-carbon molecules, which are isomers of each other. These are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.

In step 5, the enzyme triphosphate isomerase converts dihydroxyacetone phosphate into glyceraldehyde 3-phosphate.

(Remember, since we have now 2 three-carbon molecules, so there is double amount of each product from now. For instance, if one ATP is produced from one three-carbon molecule, there are two ATP molecules produced in total.)

Step 6:

Glyceraldehyde 3-phosphate is converted to 1,3-bisphosphoglycerate. The enzyme that catalyzes this reaction is called glyceraldehyde phosphate dehydrogenase. Hydogen ion is released, and NAD + Pi come in. Pi is donated to the glyceraldehyde 3-phosphate, and it is attached to the 1st carbon. NAD picks up the hydrogen ions. What we get is 1,3-bisphosphoglycerate.

Step 7:

The phosphate is removed from 1,3-bisphosphoglycerate, and 3-bisphosphoglycerate is formed. The phosphate that has been removed is attached to the ADP that comes in, so it becomes ATP. The enzyme that catalyzes this reaction is phosphoglycerate kinase.

Step 8:

The enzyme phosphoglyceromutase removes the phosphate from the third carbon of the 3-phosphoglycerate, and attaches it on the 2nd carbon. Thus, 3-phosphoglycerate becomes 2-phosphoglycerate.

Step 9:

2-phosphoglycerate is converted to phosphoenolpyruvate by enolase. During this reaction, water is released.

Step 10:

Phosphoenolpyruvate (PEP) looses its phosphate. This phosphate is donated to ADP, so it becomes ATP. The enzyme that catalyzes this reaction is called pyruvate kinase. The end product of glycolysis is pyruvate, which is used later in cellular respiration.

Glycolysis (THE BIG PICTURE)

What is glycolysis and why is it important?

Our cells obtain their energy from glucose. However, they cannot use it directly. First, they need to transform the energy from glucose to the form of energy that they can use. Cells use energy in the form of ATP. Thus, a cell transforms the energy in glucose to ATP, the form of energy that they can utilize. The process in which this occurs is cellular respiration. Glycolysis is the initial step of cellular respiration. The end products of glycolysis are used further during cellular respiration. Therefore, glycolysis is very important.

What is made and what is used during glycolysis?

Glycolysis uses 2 ATP molecules, but it makes 4 ATP molecules. Thus, our net gain will be: 4 ATP - 2 ATP = 2 ATP. During glycolysis, the cell also produces two NADH molecules. Water is also released.

Where does glycolysis occur?

Glycolysis occurs in the cytoplasm of the cell:

PLEASE, CHECK OUT MY VIDEO ABOUT THE BIG PICTURE OF GLYCOLYSIS

ATP - adenosine triphosphate

The structure of ATP
ATP stands for Adenosine triphosphate (as you can see from the title :)). What does that mean? Adenosine refers to the nucleotide adenine (the same type of adenine that is present in our DNA!) bond to ribose (the same type of sugar that is present in RNA!)
There are three (tri = three) phosphate groups attached to adenosine. All of them are negatively charged, which makes ATP an unstable molecule.

What do we need ATP for?

ATP is an energy carrier. It provides energy for all cells activities. For instance, if we want to contract a muscle, proteins in the muscle cells need ATP. Active transport into and out of the cell, such as phagocytosis or pinocytosis, also requires energy. This energy is provided by ATP.

How? Well, it transfers a phosphate group. This occurs during ATP hydrolysis. When the molecule of ATP is hydrolyzed, a phosphate is transferred and energy is released. The picture below shows how that looks like.

Please click here to watch my video about ATP

Transcription and translation

The DNA is divided into genes, which contain instruction for making proteins that make up a human. Thus, the instructions from genes in the DNA are used to make proteins. This process is called the central dogma, and it is divided into transcription and translation (described below:))

TRANSCRIPTION: Transcription occurs in the nucleus. The DNA is like a cookbook full of different recipes (genes/segments of DNA) that contain instructions about how to make proteins. Thus, if we want to make a protein, we need to copy the recipe (information in a gene) in the DNA. This is what transcription is all about.

An enzyme called RNA polymerase moves down the DNA and copies the information in it. The transcript of this information is called the messenger RNA (mRNA). However, we need to alter it a little bit before it can leave the nucleus. We need to add 5′ cap and poly(A) tail, and we must get rid of parts that don’t code for a specific amino acid.

TRANSLATION: Translation occurs in the cytoplasm. When the mRNA leaves the nucleus, it enters a ribosome. The ribosomes are protein factories. The mRNA moves through the ribosome. The amino acids that are needed to make the protein are brought by transfer RNA (tRNA). There are many types of tRNA, and each type attaches to a specific amino acid.

The tRNA attaches to the codon (three nucleotides that code for specific aminoacids) on the mRNA, and leaves the amino acid (see the picture below). This way, amino acids are bonded together, forming a polypeptide chain (a protein). This protein is later used in our body.

PLEASE CHECK OUT MY VIDEO ABOUT THE CENTRAL DOGMA HERE :)

The structure of proteins

Amino acids

Proteins are made of amino acids, which are bonded together by bonds called peptide bonds. The picture below depicts an amino acid.

As you can see, an amino acid consists of an amino group (NH2), a carboxyl group (COOH) and a variable, which is also called R. The variable is different in every amino acid, and this is why each of them is unique. 

The structure of proteins

The shape (conformation) of a protein determines what job it preforms. There are four levels of protein structure, all of them discussed and pictured below :).

PRIMARY STRUCTURE: The primary structure refers to the sequence of aminoacids in the protein. The amino acids are bond together by peptide bonds and thus form a long chain called a polypeptide chain. This chain of amino acids is an example of primary structure of a protein.

SECONDARY STRUCTURE: The secondary structure refers to a protein chain that is coiled up, either as alpha helix or beta pleated sheet (pictured below). The chain coils up because of the hydrogen bonds between the amino acids.

TERTIARY STRUCTURE: The tertiary structure is the three-dimensional (not just flat) conformation (shape) of a protein. It determines the specifity of the protein, and some factors that contribute to the tertiary structure are for example hydrogen bonds between R-groups, Ionic bonds between R-groups or disulfide bonds between cysteine amino acids.

QUATERNARY STRUCTURE: The quaternary structure refers to proteins made up of more than one polypeptide chains. An example of that is hemoglobin, which is essential in order to carry oxygen in our blood. 

PLEASE, CHECK OUT MY VIDEO ABOUT PROTEIN STRUCTURE :) 

Hydrogen bonds

The structure of a water molecule

To better understand the hydrogen bonds, let's first look at a model of a water molecule (pictured below).

 The water molecule is made of two hydrogen atoms and one oxygen atom. They are sharing the electrons. However, since the oxygen atom has a greater mass than the hydrogen atom, it exerts a stronger pull on the electrons than the hydrogen does, so the electrons spend most of their ''time'' closer to the oxygen. As a result of that, oxygen becomes negatively charged, and hydrogen becomes positively charged. Since the water molecule has two opposite poles , it's called a polar molecule or a dipole.

Hydrogen bonds

Now, when we have many (DIPOLE!) water molecules next to each other, the (positively charged) hydrogen atoms from one water molecule are attracted by the (negaltively charged) oxygen molecules. In other words: there is a force of attraction between them.
THE FORCE OF ATTRACTION BETWEEN A POSITIVELY CHARGED HYDROGEN ATOM AND NEGATIVELY CHARGED OXYGEN ATOM (FROM ANOTHER MOLECULE!)IS AN EXAMPLE ON A HYDROGEN BOND. Please look at the image below to get a better understand how hydrogen bonds look like/work (the green lines/dots = hydrogen bonds :))

The hydrogen bond is called the hydrogen bond because it refers to the force of attraction of a hydrogen atom (which is positively charged because it is a part of a polar/dipole molecule, such as water). However, the negatively charged atom doesn't have to be an oxygen atom. Hydrogen bonds can also be formed between a hydrogen and fluorine or nitrogen.

Why did I include the post about hydrogen bonds in this blog(which is supposed to be about biology:))?

It seems like it doesn't make sense to learn chemistry when our main interest is biology, but the truth is that we must know some chemistry if we want to understand biology.
The next post that I plan to make is going to be about proteins. Understanding hydrogen bonds is crucial if we want to understand the structure of proteins.