Trios Phosphate Isomerase Structure and Function

Triose Phosphate Isomerase is an enzyme which is extremely useful in the glycolytic pathway. Glycolysis is a metabolic pathway where organisms extract energy in the form of ATP during the conversion of glucose into pyruvate and lactate. Glycolysis helps supply the body with energy that it needs.Trios Phosphate aids in catalysis by binding tightly to the enediol transition state. To convert GAP to the enediol intermediate, a proton is abstracted from C2 by a a Glyceraldehyde 3 phosphate base, the active site which is near carboxyl group, and the carbonyl oxygen atom is protonated by an acid.[4]

The process is better understood when followed step by step. First, glyceraldehyde-3-phosphate binds to the active site near the carboxyl group, then enediol intermediates (Glu 165) picks up the C2 photon and in the process HA donates a proton to make a carbonyl oxygen. Then a proton is returned and once it is accepted a DHAP is made.Its quaternary structure is a homodimer, which means it is a protein composed of two polypeptide chains. Trios Phosphate has a very interesting structure that is important to its function. Its secondary structure has 14 alpha helices and 8 beta sheets. Its tertiary structure is an alpha-beta barrel in which beta barrels are surrounded by alpha helices in between the beta strands. They are intertwined in a way and they create a barrel shape which is called “TIM Barrel”.

This is a picture of an active site which is Glu 165 and in this spot is where the enzyme grabs the C2 proton.

The photo above shows the “TIM Barrel” shape in which the alpha helices wrap around the beta sheets. In proteins with this “TIM Barrel” structure, the loops at the C-terminal ends of the parallel beta-strands form the active site.

The loop formed by residues 167 (circled) to 176 (labeled), close over the active site and it does not allow the phosphate to leave during the enediol intermediate. Without the loop, the phosphate could escape and the DHAP would not be made.

Jolecule article

Fun With Jolecule: The Glucocorticoid Receptor

      In order to research and explore protein structures, I had to utilize a protein model visualizer called Jolecule, on http://jolecule.appspot.com/ . Once on the main page, I clicked on the tutorial to familiarize myself with the visualizer, and then first examined the myglobin protein. Then, I looked through the "garden" feature of the website, and ultimately chose the glucocorticoid receptor protein to take a closer look at.
      The glucocorticoid receptor protein is responsible for controlling stress response within the nucleus of cells. The interaction between this receptor and actual glucocorticoids is referred to as a signal transduction process, which means that it involves the interaction of extracellular signaling molecules to receptors that trigger events inside the cell. This process can be broken down into steps, which helps to show the many functions of the glucocorticoid receptor. These steps can include: the transformation of a receptor into an active form as a result of specific interactions with steroid hormones; homo-dimerization, or the joining of two molecular subunits to create one dimer; DNA bindings to specific hormone responses; and modulation of expression levels within linked genes. Overall, the glucocorticoid receptor plays an integral part in the function of the cell as well as the interactions of steroid hormones within the cell, and that is why I find this protein to be interesting.
      The glucocorticoid receptor protein, in jolecule, is shown to be made up of several parts. These parts include the N-Terminal domain (the DNA), the DNA binding domain (DBD), a hinge region, the Ligand binding domain (LBD), as well as the C-Terminal domain (the end). In order for the receptor to work, the DBD has to bind to the N-Terminal domain, which occurs through the interaction of proteins in the DNA as well as the DBD. Then, the LBD is connected to the DBD through a hinge region which could be simple or complex. The interactions between the DNA as well as the DBD and LBD when coming into contact with a steroid hormone are what affect the dimerization of molecules as well as the affinity of binding DNA.
      Included below are some screenshots of the glucocorticoid receptor in the Jolecule model visualizer.

The above photo depicts the interactions between the DNA helix and the proteins of the DNA binding domain. The DNA helix is shown as the purple strands and the DNA binding domain is shown through the blue strands.

The above photo depicts the glucocorticoid receptor in relation to all of its components. The N-Terminal domain, or DNA, is shown as the purple strands. The DNA binding domain is shown as the blue strands, and the Ligand binding domain is shown as the blue strands. The yellow strands are the ligands that are involved in the process. 

The above photo depicts the hinge region of the glococorticoid receptor that binds the DBD to the LBD. In this case, the hinge region of the receptor involves the atom zinc.

Trypsin enzyme structure and function

                Trypsin: A protein digestive enzyme

Digestive enzymes are interesting because they break down certain types of molecules. Proteins are broken down by protease enzymes while carbohydrates are digested by carbohydrate enzymes. Each enzymes has a very unique structure that is suitable for its function. Enzymes like Trypsin have an active site where substrates are broken down into smaller amino acids. Protein digestion is very important for our body and Proteins are essential for life.

Trypsin is produced by the Pancreas. It is a protein digestive enzyme that works in optimum temperature. Trypsin helps the breakdown of large protein molecules into smaller amino acids. In the duodenum, Trypsin breaks down Proteins into Polypeptides because these type of digestion is necessary for the absorption because Proteins are too large to be absorbed by the lining of the small intestine.

Trypsin cleaves the peptide chains mainly the carboxyl side of the amino acid.

The above screenshot shows the structure of Trypsin. These types of Protein structures can be in Jolecule, a model visualizer. Trypsin has both Alpha-helix and Beta-pleated sheets. Trypsin is made up of all 20 amino acids, but the active side of the enzyme involves Glutamine and Valine. The active sites of Glutamine and Valine before and during the substrate is being catalysed is shown below.

The picture on the left shows the active site of Glutamine in the Trypsin Enzyme. The picture on the right shows the active site when it binds with the substrate which is represented by the red circle. During these process, dehydration synthesis occurs where water molecules are being released to break bonds. In these case, the oxygen of Glutamine binds with the substrate. The peptide bonds are broken down and the Oxygen comes from the carboxyl side of Glutamine.

The picture on the left shows the active site of Valine and the picture on the right shows the active site when it binds with the substrate. The process is similar to the ones related to Glutamine. The oxygen from the carboxyl side of Valine is being used and these is another side of the active site that does similar functions in breaking bonds that the Glutamine active site does. The process of breaking down protein into polypeptides are increased due to the sides of the active sites where different amino acids joins with the substrate for the final product.

Dihydrofolate Reductase Protein Structure and Function

I investigated the dihydrofolate reductase protein. This protein was very interesting to me because it is used for drug therapy and was the first to help in cancer chemotherapy. Knowing this I looked at the protein’s structure and function to support its role in cancer chemotherapy.

Dihydrofolate reductase is a small enzyme that plays a significant role in DNA construction. Dihydrofolate reductase controls the state of folate, an organic molecule that transports carbon atoms. By reducing dihydrofolic acid to tetrahydrofolic acid. Dihydrofolic acid is a folic acid derivative which transforms to tetrahydrofolic acid by the dihydrofolate reductase protein.  Tetrahydrofolate is needed to make purines and pyrimidines both being building blocks of DNA and RNA

The dihydrofolate reductase has a unique structure. It contains eight beta sheets and four alpha helixes. Dihydrofolate reductase has a long channel that binds to folate at one end and NADPH at the other end.  The protein encloses side chains around folate and NADPH resulting in them being in a very tight position close to each other. This way it can shuttle hydrogen atoms from NADPH to folate, reducing it. The backbone folding of this protein is mainly due to the beta pleated sheets which explains why the molecule is so rigid. This protein is highly stable due to the formation of the dimer. A dimer is a quaternary structure made by two non-covalently bounded macromolecules such as proteins or nucleic acids. In the beta sheets dimers interact to produce tight, high packing density.

Drugs, like aminopterin, bind to dihydrofolate reductase much tighter than folate and produce better clinical outcomes. These drugs kill active growing cells rather than inactive non growing cells and will have a major impact on cancer cells, considering they reproduce at a very high rate. Dihydrofolate reductase plays a major role in battling cancer because drugs are able to bind to it a thousand times tighter, preventing growth of certain cells.

Shown above is the overall Dihydrofolate Reductase protein structure.

Depicted above are the side chains that wrap all around the protein. Some of the side chains are circled in blue. The red circle shows one particular side chain of the Asn amino acid. Remember side chains enclose folate and NADPH to create a tightly bound protein.

Shown above are the beta pleated sheets in yellow and alpha helixes in lavender. There are more beta sheets than helixes therefore producing a more rigid protein structure.

Shown above are binding sites. These binds help in creating the shape of the protein.

Shown above is the primary structure of the Dihydrofolate reductase before it advances to its later protein structures. It contains Nitrogen, Hydrogen, and Oxygen.

fun with jolecule:The Antibody

The protein that I will be exploring in this article is the antibody. I find the antibody interesting because of the high amount of variability in terms of different antibodies that all seek to perform similar functions like neutralizing toxins or viruses.These toxins or viruses are called antigens..  Even with the high amount of variability in antibodies all antibodies share parts of their

Structure .Antibodies are proteins produced in vertebrates ( by b cells) mostly made up of beta pleated sheets with a small number of alpha helices which you can see in the general overview of the antibody above. They are also covered in short chains of carbohydrates called glycoproteins (which I have also shown above). Antibodies are made up of two light chains and two heavy chains of proteins. These chains make a “Y” shape(to the left the the intertwined heavy chains are circled in blue and the light chains are in red). The tips of the “Y” have a region that is of high variability among different antibodies. This means in different antibodies in the tips of the Y the primary structure varies. This is because the tips contain the areas that bind to antigens called antigen binding sites.This also explains the reason why antibodies need to have a high amount of variability in the primary structure of the tips.There are a wide amount of things the body would consider an antigen that an antibody would need to bind to and if the structure of every antibody was exactly the same it would not be able to complete that function.

Above three binding sites are circled in red These three sites are rearranged in different antibodies to achieve the effect of binding to a specific antigen.These sites are called paratopes and they bind to epitopes on antigens. The primary structure of the paratope causes the site to fold in a way that will allow the site to bond to the epitope.  By binding to an antigen an antibody can change the structure and therefore the function of a part of an invading virus, for example, and render it unable to invade the cell.

Raquel Rubisco Protein Article

The enzyme ribulose bisphosphate carboxylase/oxygenaseis (Rubisco) is the most abundant enzyme on Earth and is essentially the most important. It is known as the “carbon fixer”. Carbon is essential for all life, however it is locked in oxidized forms in the atmosphere and earth, such as carbon dioxide or carbonate minerals. This oxidized carbon must be "fixed" into more organic forms to be useful for organisms. Commonly found in plants, Rubisco creates organic carbon from the inorganic carbon dioxide in the air with the help of sunlight. This central task of carbon fixation is known as photosynthesis in plants. It is a very important enzyme and is essential for the carbon cycle. Even though this enzyme has such a central importance, it is inefficient because it works very slowly compared to other enzymes. Plant cells compensate for this slow rate by producing lots of the enzyme. Chloroplasts are filled with Rubisco, which makes it the most plentiful enzyme on Earth.

Rubisco takes carbon dioxide from the air and attaches it to ribulose biphosphate, a short sugar chain with five carbon atoms. This six-carbon molecule is extremely unstable and rubisco immediately clips the lengthened chain into two identical phosphoglycerate pieces, each with three carbon atoms. Most of the phosphoglycerate made by rubisco is recycled to build more ribulose bisphosphate, while some is skimmed off to make sucrose and feed the rest of the plant. The 3-phosphoglycerate can be used to produce larger molecules such as glucose.  

During the night, the Rubisco active sites are blocked by inhibitors or misfired reactants, which ensures that it will only be active during the day when sunlight is available. The active site of Rubisco is centered around a magnesium ion. The magnesium ion is free to bind to both ribulose bisphosphate, holding onto two oxygen atoms, and the carbon dioxide molecule that will be attached to sugar. Because Rubisco may lack some specificity, Rubisco may attach an oxygen molecule instead of the carbon dioxide molecule to the sugar chain, forming a faulty oxygenated product and will have to go through a series of reactions to correct the mistake.

This is the overview of the protein Rubisco. This shows two copies of the large chain and you can also see the active sites. The alpha-helixes and beta-pleated sheets are clearly visible.

This is an image of ribulose biphosphate, a short sugar chain with five carbon atoms. A carbon dioxide molecule will be binded to this sugar.

This is an image of the magnesium atom in the center of the active site. It is binded to the five carbon sugar pictured above.

This is a picture of the magnesium atom about to bind the carbon dioxide molecule to the five carbon sugar. The addition of this carbon dioxide molecule will cause the newly formed 6 carbon molecule to break down into two identical 3-phosphoglycerate pieces.

Connor DNA Ligase Artcile for Jolecule

DNA Ligase

DNA Ligase plays an extremely important biological function. This enzyme has the responsibility of joining strands of DNA together, and is therefore essential to life and reproduction. The role of DNA ligase is most often to play its key part in DNA replication, in which it combines multiple strands of DNA by forming bonds known as phosphodiester bonds, using AMP.  In addition, DNA Ligase repairs breaks between strands of DNA, and does this by catalyzing the formation of phosphodiester bonds just as it does during the DNA replication process. These bonds are created when two hydroxyl groups in phosphoric acid form two ester bonds. Phosphodiester bonds are essential in DNA and RNA as they create the backbone between nucleic acids which form them.

    DNA ligase’s structure is what allows it to function as it does. DNA ligase contains an AMP nucleotide attached to the active site of DNA ligase that is transferred to the phosphate group within the enzyme and bonded to it. This bond can then be broken up to form three OH bonds and release the AMP. After this is done ATP must be added to complete the role of DNA ligase bonding the strands of DNA. The tertiary structure of DNA ligase is what allows it to function as it does.  The side chain containing AMP allows it to form phosphodiester bonds.

Pictured above is DNA ligase. Its overall structure is essential to its functionality as an enzyme in the DNA construction process. It works best in cold environments as two strands of DNA must stay with the ligase long enough for the chemical bonds to be made, and heat would both denature this enzyme’s structure on its tertiary level and speed up the DNA molecules to a higher rate of movement.

The picture above indicates the location of AMP, the part of the molecule crucial in the formation of  the phosphodiester bonds that connect the strands of DNA after energy has been added to the ligase.

The focus of this picture is the binding channel, in which both strands of DNA must go through in order to be bound by the ligase. The binding channel is the ring depicted towards the center of the photo.

Sample Jolecule blog post

Lysozymes

            In order to explore protein structures I went onto a protein model visualizer, called Jolecule, on http://jolecule.appspot.com/.  Once on the main page, I clicked on the “myoglobin” button, and then the “garden” link in the upper right corner.  This last link brought me to a variety of proteins to select from and learn about.  After I have looked through them, I chose to research the Lysozyme protein.  

            Lysozymes are small protein enzymes that bind to polysaccharide chains and break them apart by hydrolysis.  These enzymes protect humans from danger of bacterial infection by attacking and destroying the cell walls of the bacteria.  The bacteria itself constructs a tough skin of carbohydrate chains (sugars) that are interconnected by short peptide strands.  In order to fight the bacteria, the lysozyme breaks the carbohydrate chains of the bacteria, which in turn, destroys the structural integrity of the cell wall and causes the bacteria to burst.  However, as efficient as it is in killing bacteria, the lysozyme is too large of a molecule to travel between cells, that it cannot rid the entire body of disease.  Lysozymes occur in plant and animal tissues and in secretions such as tears, saliva and mucus.  Also it is greatly found in egg whites.  It is found in our tears, and mucus to resist infection on exposed surfaces.  Lysozyme also provides protection in the blood because blood is the worst place for bacteria to grow.  In general Lysozymes protect many places that are rich in potential food for bacteria.  As well, Lysozyme is added to digest cell debris and release the inclusion bodies. 

Furthermore, Lysozyme is a crystal structure with two structural domains.  One is made up of mainly alpha helices, and the other is mainly beta strands.  The boundary between the two domains forms a split where the substrate binds.  Lysozyme adds a molecule of water to the bond between two sugars, which breaks the bond.  This is catalyzed by two amino acid side chains in the active site of the enzyme.  These active sites are glutamate 35 and aspartate 52.  

- This is the overall picture of the lysozyme protein with the polysaccharide substrate in the center. 

- This is one of the glu-35 active sites of the enzyme, which would lie next to the polysaccharide.  

- This is one of the asp-52 active sites of the enzyme, which would lie next to the polysaccharide.  

Hardy-Weinberg Model Presentation

Hardy Weinberg Equilibrium Modeling

Herdy-Weinburg Equilibrium Presentation - Adil Rashid

Hardy-Weinberg Equilibrium Presentation T'ea Cameron

Hardy-Weinberg Equilibrium Project Natalia Rodriguez

Hardy Weinberg Equilibrium Project Connor

Hardy-Weinberg Equilibrium Presentation Raquel

Hardy-Weinberg Equilibrium Presentation Russell

T and A project

Natalia and Sana's Guppy Argument

Russell and Harold Guppy Presentation

Raquel and Connor's Guppy Argument

How to Blog Safely

Remember that blogs are public forums and that anything you post to the Internet stays there...ostensibly for eternity. With that in mind, let's follow a few basic rules:

1. Set up your account using only your first name, or an alias (in which case you should email me so I know which posts belong to you). Don't use your full name.
2. No using pictures of yourself in your profile. Don't give out a phone number or home address.
3. Treat the blog like our classroom (respectful language and conduct in relation to other bloggers is a must).

"Now you stick with that, and everything else is cream cheese." -- Coach Finstock, Teen Wolf (1985)

Forget the MTV remake. Michael J. Fox rules.