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E-mail the story Catalyst made from iron can drive an important reaction for making organic compounds. Your friend's email. Your email. I would like to subscribe to Science X Newsletter. Learn more. Your name. Note Your email address is used only to let the recipient know who sent the email. Your message.
Plietker deserves credit for his this nice piece of work, and the book will have a prime spot on my shelf. If you do not receive an email within 10 minutes, your email address may not be registered, and you may need to create a new Wiley Online Library account. If the address matches an existing account you will receive an email with instructions to retrieve your username. Skip to Main Content. Bernd Plietker. First published: 13 August About this book This first comprehensive book to cover this exciting field also deals with the biological aspects, such as enzymes with iron.
Proteins e. To understand how ferritin or any of the many molecules that you will encounter in this course and throughout your experience in the sciences performs its job, we must be able to visualize the three-dimensional structure of the molecule, and understand the relationship between the structural features and the function of the molecule. Furthermore, we must be able to communicate this image of the three-dimensional structure to others who want to learn about the molecule's structure and function.
There are several strategies that we could use to visualize the ferritin protein's three-dimensional structure, and communicate this image to others. We could make three-dimensional models to depict the structure of ferritin, but these models would be inconvenient for distributing the information widely. The most common formats for distributing information today- in books and on computer screens- necessitate that the image be displayed in two dimensions.
Of course, there are many difficulties involved in converting all of the important structural information about a molecule into an easily understandable two-dimensional representation. No two-dimensional representation can show a three-dimensional structure in its entirety. Hence, a variety of molecular representation formats have been developed; each of these representations is designed to show a particular aspect of a molecule's structure.
Thus, to illustrate a specific point about a molecule's structure, the type of representation must be chosen carefully. To provide a comprehensive view of a molecule's structure, multiple representations are used. In this tutorial, the 2D-ChemDraw, stick, CPK, and ribbon representations are used to examine the three-dimensional structure of ferritin. These four types of representations are described in the blue box, below.
Graphical computer modeling has greatly improved our ability to represent three-dimensional structures. One of the goals of graphical computer modeling is to create the computer-generated image such that the image seems three-dimensional. By replicating the effect of light on three-dimensional objects, computers can give the impression of depth to simulate the three-dimensional aspect. The ability of interactive molecular viewing e. By interactively rotating the molecules, a clear picture of the three-dimensional structure emerges. In addition, this increases our chemical intuition by looking at two-dimensional images and visualizing the three-dimensional structure in our brains.
This tutorial uses different types of structural representations Figure 2, Table 1 , such as 2D-ChemDraw, stick, CPK, and ribbon, to illustrate the structure of ferritin. PDB files are also available for viewing the molecules interactively. By using these various representations to study the structure of ferritin, you will become familiar with the different types of information given by each type of molecular representation, as well as the strengths and limitations of each representation.
This figure shows an alpha-helix from the " Hemoglobin and the Heme Group: Metal Complexes in the Blood " tutorial in four different types of computer-generated molecular representations. Although all four representations depict the same molecule, they look very different and offer different information about the molecule's structure see Table 1.
Note: In the 2D-ChemDraw, stick, and CPK representations, carbon atoms are shown in gray black , nitrogen atoms are shown in blue, and oxygen atoms are shown in red. In this figure, hydrogen atoms light blue are shown in the 2D-ChemDraw representation but hydrogen atoms are not shown in the other representations. By examining the four representations in Figure 2, you can see that each picture tells us something different about the structure of the molecule.
For instance, if we wanted to know how the atoms in an alpha helix are connected to one another, we would use the ChemDraw or stick representation. To see the relative sizes of the atoms in an alpha helix, we would use the CPK representation. Descriptions of the four types of representations, their major strengths, and their drawbacks are given in Table 1, below. This table lists some of the important attributes of the four types of representations pictured in Figure 2 above. Now we shall use the molecular-modeling tools representations described above to zoom in on the ferritin protein and study its structure.
We will begin at the smallest level of protein structure, by using 2D-ChemDraw representations to show how atoms are combined to make amino acids. Then we will use all four representations to show how amino acids come together to form the protein subunits known as peptides, and how the sequence of amino acids determines the shape of the peptide. Finally, we will use the ribbon and CPK representations to show how 24 peptide subunits are combined to make the hollow-sphere shape and channels in ferritin.
The basic structural features of proteins that you will learn about in this tutorial will provide a foundation for understanding the structure and function of any protein. Because proteins are a tremendously important class of biological molecules, you will study many different proteins in these tutorials and in your other coursework and research. All proteins consist of chains of amino acids. There are 20 different amino acids that are available to be incorporated into proteins. The side chains of the 20 amino acids have different properties, which in turn give different properties to the amino acids.
For instance, side chains may be charged e. On the left is a two-dimensional ChemDraw model of an amino acid. The carboxylic acid group is shown in blue, the amino group is shown in purple, and the central carbon atom is shown in red. The green "R" represents the side chain, which is different for each amino acid. On the right is a two-dimensional ChemDraw model of leucine, one of the twenty amino acids available for building proteins.
Leucine differs from the other amino acids only in its side chain, shown in green. Amino acids are linked together to form chains known as peptides. Figures 4 and 5 show the three amino acid residues leucine, alanine, and glutamate Leu-Ala-Glu that are bound together and form a part of the peptide subunit found in ferritin.
In this figure, the functional groups that form peptide bonds in the amino-acid sequence Leu-Ala-Glu are shown in blue. In this figure, the backbone of the amino-acid sequence Leu-Ala-Glu is shown in purple, and the side chains are shown in green. Peptides may be very long chains of amino acids. There are residues in each peptide subunit in human ferritin.
Fundamentals and Applications
The side chains of amino acids in a peptide can interact with one another, causing the peptide to fold. The shape of the peptide depends on where the peptide is folded, which in turn depends on the sequence of amino acids in the peptide i. One common example of folding in a peptide is the alpha-helix motif, which is common in many proteins. Recall from the " Hemoglobin and the Heme Group: Metal Complexes in the Blood " tutorial that an alpha helix is formed when there is a regular pattern of side chains that form hydrogen bonds with one another. Figure 6 shows the hydrogen-bonding interactions between amino-acid residues that give rise to the helical structure shown in the ribbon representation.
This is a close-up of part of an alpha helix in a peptide chain of ferritin. The helical shape is held by hydrogen bonds represented by green dotted lines between the -NH and -CO functional groups in the backbone. In this figure, the ribbon representation showing only the trace of the backbone is superimposed on a ball-and-stick representation, in which the non-hydrogen atoms are shown as spheres and the bonds are shown as sticks.
Note: The carbon atoms are gray, the nitrogen atoms are blue, and the oxygen atoms are red in this model. Hydrogen atoms are not shown. Below are two representations of the peptide subunit in ferritin.
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The first representation Figure 7 is a CPK model of the peptide chain. The CPK representation gives an approximate volume of the subunit. Figure 8 shows a ribbon representation of the peptide. The ribbon representation is useful for showing the alpha helices in the peptide.
This is a molecular model of a peptide chain in the ferritin protein, shown in the CPK spacefilled representation. In this representation all of the heavy non-hydrogen atoms are displayed. CPK pictures represent the atoms as spheres, where the radius of the sphere is equal to the van der Waals radius of the atom. Note: The carbon atoms are gray, the nitrogen atoms are blue, the oxygen atoms are red, and the sulfur atoms are yellow in this CPK model.
Hydrogen atoms are not shown in this figure. Another common representation for proteins and peptides is the ribbon, which traces the backbone of a protein or peptide. This representation does not include the atoms in the side chains of the residues and is often used to represent the three-dimensional structure. Notice the bundle of helical, or coiled, segments of the backbone.
To make the ferritin protein, 24 peptide subunits Figures are assembled into a hollow spherical shell Figure 9. The sphere that is formed is approximately 80 Angstroms in diameter, and the walls are approximately 10 Angstroms thick. The molecular weight of ferritin i.
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Channels i. As we shall see, these channels are critical to ferritin's ability to release iron in a controlled fashion. Two types of channels exist in ferritin. Four-fold channels such as the one shown in the center of Figure 9 occur at the intersection of four peptide subunits.https://boggrerasi.tk
Three-fold channels such as those shown on the outskirts of Figure 9 occur at the intersection of three peptide subunits. The two types of channels have different chemical properties, and hence perform different functions, as we shall see later "Release of Iron" section. This is a molecular model of ferritin in the CPK representation. CPK pictures represent the atoms as spheres, where the radius of each sphere is equal to the van der Waals radius of the atom.