Proteins are essential to organisms and many processes that keep people functioning and living every day. Proteins are comprised of polypeptides that are folded into different forms to fulfill a biological function. Each polypeptide is part of a single, linear chain of amino acids that are bonded by peptide bonds. The amino acid sequence of these polymer chains encodes the sequence of genes. These different genes can code for proteins that make enzymes, muscle structure, and even mechanical functions.
Protein primary structure is composed of amino acid residues. There are 20 different amino acids that can compose this amino acid sequence. The non-covalent interactions and the structure of the peptide bonds in these primary sequences help determine how the protein folds into its secondary structure. The bond’s rotation is characterized by the φ (PHI), ψ (PSI), ω (omega) rotation about the peptide bonds (Figure 1). The secondary structure shows the local spatial arrangement of the polypeptide chain characterized by the α-helix, the β-sheet, the random coil and the β-turn. Unlike the tertiary structure of a protein, these secondary structures do not dictate function. The tertiary structures of a protein fall into two major classes: the fibrous proteins and the globular proteins. The fibrous proteins are usually found with membranes. Globular proteins, on the other hand are typically water-soluble like myoglobin. The tertiary structure of a protein compiles to from the quaternary structure of proteins. The quaternary structure is comprised of multiple tertiary structure proteins forming a larger protein together. The structure can depend on the active site of each domain, the multiple binding sites within the structure...
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...actually fold.
Works Cited
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Macromolecules are define as large molecules of structures found in living organisms. There are four types of macromolecules, which are proteins, carbohydrate, nucleic acid, and lipids also known as fats. Carbohydrates, proteins, and nucleic acids are made of monomers, which are structural units that eventually attached together to form polymers (Dooley 20). For instance, proteins are made of amino acids, which are monomers. In addition, it has a complex structure, which consist of four different levels, primary, secondary, tertiary, and quaternary. The first structure of protein is the primary structure, which is the sequence of amino acid, while in the secondary structure alpha and beta helices are formed. The structure, in which a protein becomes active, is in the tertiary structure, which is where polypeptide subunits fold. Meanwhile, only certain proteins have the quaternary structure, which is when, more than one polypeptide folds. Proteins are prominent macromolecules mainly because of their numerous functions. For instance, proteins are known for increasing the rate of reactions due to that enzymes are a type of protein. In addition, they are a form of defense mechanism such as they attack pathogens, which cause diseases. In other words, scientists study and gain more insight on certain illness and how to prevent them by using proteins. For example, in a recent study,
Wissmueller S., Font J., Liew C.W., Cram E., Schroeder T., Turner J., Crossley M., Mackay J.P. and Matthews J.M. (2011). Protein-protein interactions: analysis of a false positive GST pulldown result. Proteins. 79 (8), pp. 2365-2371.
Shaevitz, J. W., S. M. Block, and M.J. Schnitzer. 2005. Statistical Kinetics of Macromolecular Dynamics. Biophysical Journal 89: 2277
Sequence and structural proteomics involve the large scale analysis of protein structure. Comparison among the sequence and structure of the protein enable the identification on the function of newly discovered genes (Proteoconsult, n.d.). It consists of two parallel goals which one of the goals is to determine three-dimensional structures of proteins. Determine the structure of the protein help to modeled many other structures by using computational techniques (Christendat et al., 2000). This approach is useful in phylogenetic distribution of folds and structural features of proteins (Christendat et al., 2000). Nuclear magnetic resonance (NMR) spectroscopy is one of the techniques that provide experimental data for those initiatives. It is best applied to proteins which are smaller than 250 amino acids (Yee et al., 2001). Although it is limited by size constraints and also lengthy data collection and analysis time, it is still recommended as it can deliver strong results. There are two types of NMR which are one-dimensional NMR and two-dimensional NMR. One-dimensional NMR provides enough information for assessing the folding properties of proteins (Rehm, Huber & Holak, 2002). It also helps to identify a mixture of folded and unfolded protein by observing both signal dispersion and prominent peak. Observation in one-dimensional spectrum also obtains information on molecular weight and aggregation of molecule under investigation. In spite of this, two-dimensional NMR are used for screening that reveal structural include binding, properties of proteins. It also provides important information for optimizing conditions for protein constructs that are amenable to structural studies (Rehm et al., 2002). NMR is a powerful tool which it w...
(Kesssel,A. and Ben-Tal N. (2011) Introduction to Proteins: Structure, Function and Motion, London: CRC Press)
In summary, this excerpt went over how proteins are a linear polymer of amino acids linked together by peptide bonds. There are various interactions between the amino acids, which are mostly non-covalent, that stabilize the structure of a folded protein. There are 20 unique amino acids found naturally and can be grouped into three categories based off the nature of their R groups located on the side of the amino acids. Hydrophilic, hydrophobic or amino acids with a special R group which are composed of cysteine, glycine and proline. The Alpha helix and beta sheet are the most abundant structures of protein secondary structures. These stabilize hydr...
Campbell, M.K., Shawn, S.O. (2012). Biochemistry, 7th Edition. The Behaviour of Proteins: Enzymes. Pg 139-159.
NMR experiments can provide useful structural information and probe different aspects of the molecule’s nuclear environment. Suggest two NMR experiments that may illustrate how a globular protein could respond to the changes of pH, temperature, and
...ications applied to proteins in the ER involves the addition and removal of sugar molecules. Often time’s misfolded proteins have to be glycosylated repeatedly until the correct folding is induced. This process requires a lot of energy and this is typically not a problem for the eukaryotic cell but in a environment that has limited resources the simplicity of the prokaryote could be more effective because it does not require near the amount of energy to sustain life.
In the hierarchial organisation of proteins, domains are found at the highest level of tertiary structure. Since the term was first used by Wetlaufer (1973) a number of definitions exist reflecting author bias, however all of the definitions agree that domains are independently folding compact units. Domains are frequently coded by exons and therefore have specific functionality. Among the many descriptions of protein domains the two most striking and simple are " Protein evolutionary units" and "Basic currency of Proteins".
VMD or Visual Molecular Dynamics is a computer program that can be used to design, animate, and model molecules especially organic molecules so that they can be visualized in 3-dimensional graphics for analysis and better understanding of their molecular structure and components. For the most part VMD is used to view and analyze the molecular stimulations, but the program also contains rendering tools that can be used to modify the dimensional and sequential data of the molecules. The data can be applied in various ways. Biochemists can rearrange and form amino acids to observe mutagenesis or functions of the proteins, it can also be useful to predict and understand catalytic mechanisms stimulated by proteins.
Moran, L.A. Horton, R.A. Scrimgeour, G. et al. (2014c) "Proteins: Three-Dimensional Structure and Function" In Principles of Biochemistry: Pearson New International Edition Fifth Edition ed. Edinburgh Gate, Harlow, Essex, CM20 2JE: Pearson Education Limited. pp. 133-134, 135.
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...
Garrett M. Morris and Marguerita Lim-Wilby, Molecular Docking, In Molecular Modeling of Proteins Methods in Molecular Biology, 2008, Volume 443
Proteins are considered to be the most versatile macromolecules in a living system. This is because they serve crucial functions in all biological processes. Proteins are linear polymers, and they are made up of monomer units that are called amino acids. The sequence of the amino acids linked together is referred to as the primary structure. A protein will spontaneously fold up into a 3D shape caused by the hydrogen bonding of amino acids near each other. This 3D structure is determined by the sequence of the amino acids. The 3D structure is referred to as the secondary structure. There is also a tertiary structure, which is formed by the long-range interactions of the amino acids. Protein function is directly dependent on this 3D structure.