Show dimerization of two alanines with the context of a 3d protein and make a sk
ID: 623354 • Letter: S
Question
Show dimerization of two alanines with the context of a 3d protein and make a sketch.Explanation / Answer
Here is a summary for the primary structure of a protein: I. Primary Structure: 1. It is a sequence of amino acids. 2. It is a linear polymer: linking the alpha-cacboxyl group of one amino acid to the alpha amino group of another amino acid => PEPTIDE BOND (covalent bond). 3. In some proteins, the linear polypeptide chain is cross-linked: Disulfide bonds. The primary structure is a polypeptide, in which: + each amino acid in the peptide is a residue. + there is a regularly repeating segment called the main chain or backbone,and a variable part, comprised of the side chain. Contents [show] [edit]Primary Structure The primary structure of a protein is a linear polymer with a series of amino acids. These amino acids are connected by C-N bonds, also known as peptide bonds. The formation of peptide bonds produce water molecules as a by-product when an amino terminal residue (N-terminal) loses an oxygen from the alpha-carboxyl group while the other amino acid loses two of its hydrogens from its alpha-amino group. Thus, polypeptide, or polypeptide chain, is a term that describes the multiple connected peptide bonds between numerous amino acids. Each amino acid in a polypeptide chain is a unit, commonly known as a residue. These chains have a planar backbone, as the peptide bonds have double bond characteristics due to the existence of resonance between the carbonyl carbon and the nitrogen where the peptide bonds form. The primary structure of each protein has been precisely determined by the specific genes. The C-N bond in an amino acids chain has the character of a double bond. This bond has a short length and stable. It cannot be rotated. This double-bond character can be explained structurally, in that the R groups in amino acid chains avoid steric clash. Amino acids are linked by peptide bonds to form polypeptide chain; each amino acid unit is known as a residue; a polypeptide chain constructed by the same unit is known as the main chain or backbone and a changing R group, side chains. [edit]Forces that stabilize Protein Structure Protein structures are governed primarily by hydrophobic effects and by interactions between polar residues and other types of bonds. The hydrophobic effect is the major determination of original protein structure. The aggregation of nonpolar side chains in the interior of a protein is favored by the increase in Entropy of the water molecules that would otherwise form cages around the hydrophobic groups. Hydrophobic side chains give a good indication as to which portions of a polypeptide chain are inside, out of contact with the aqueous solvent. Hydrogen bonding is a central feature in protein structure but only make minor contributions to protein stability. Hydrogen bonds fine tune the tertiary structure by selecting the unique structure of a protein from among a relatively small number of hydrophobically stabilized conformations. Disulfide bonding can form within and between polypeptide chains as proteins fold to its native conformation. Metal ions may also function to internally cross link proteins. [edit]Factors that cause denaturing 1)Temperature 2) pH Extreme temperatures will result in the unfolding of a polypeptide chain leading to a change in structure and often a loss of function. If the protein functioned as an enzyme denaturing will cause that protein to lose its enzymatic activity. As the temperature of a solution containing the protein is raised, the extra heat causes twisting and bending of bonds. As proteins begin to denature the secondary structure of the protein is lost and adopts a random coil configuration. Covalent interaction between amino acid side chains such as disulfide bonds are also lost. At high or low pH levels the protein will denature due to the lose or gain of a proton and, therefore, will lose their charge or become charged, depending on which way the pH is changed and by how much. This will eliminate many of the ionic interactions that were necessary for maintenance of the folded shape of the protein. As a result the change in structure will cause a change or loss of function. [edit]Determination of Primary Structure: Amino Acid Sequencing After the polypeptide has been purified, the composition of the polypeptide should be established. To determine which amino acid and how much of each is present, the entire strand is degreaded by amide hydrolysis (6N HCl, 1100C, 24hr) to produce a mixture of all free amino acid residues. The mixture is separated and its composition recorded by amino acid analyzer. The amino acid analyzer establishes the composition of a polypeptide by giving a chromatogram, which records the peaks of each amino acid presents in the sequence. However, the amino acid analyzer can only give the composition of a polypeptide, not the order in which the amino acids are bound to one another. To determine the amino acid sequence, it usually starts from the determination of the amino terminal of the polypeptide. The procedure is known as Edman degradation, and the reagent employed is phenyl isothiocyanate. Phenyl isothiocyanate In Edman degradation, the terminal amino group adds to the isothiocyanate reagent to produce a thiourea derivative. Treating with mild acid, the tagged amino acid is turned into a phenylthiohydantoin, and the remainder of polypeptide is unchanged. Since the phenylthiohydantoins of all amino acid are known, the amino terminal of the original polypeptide can be identified easily. However, Edman degradation can only be used to identify the amino end of the polypeptides; therefore, for polypeptides that are made up by hundreds of amino acids, it is not a practical method in general. In addition, multiple degradation rounds will build up impurities which will seriously affect the yield of peptide. High yield means not completely quantitative, and with each step of degradation, incompletely reacted peptide will mix with the new peptide, resulting in a intractable mixture. In other words, secondary structure refers to the spatial arrangement of amino acid residues that are nearby in the sequence. The alpha helix, and beta strands are elements of secondary structure. [edit]Secondary Structure Secondary structures of proteins are typically very regular in their conformation. They are the spacial arrangements of primary structures. Alpha Helices and Beta Pleated Sheets are two types of regular structures. An interesting bit of information is that certain amino acids making up the polypeptide will actually prefer certain folding structures. The Alpha Helix seems to be the default but due to interactions such as sterics, certain amino acids will prefer to fold into Beta pleated sheets and so on. For example, amino acids such as Valine, Isoleucine, and Threonine all have branching at the beta carbon, this will cause steric clashes in an alpha helix arrangement. Glycine is the smallest amino acid and can fit into all structures so it does not favor the helix formation in particular. Therefore, these amino acids are mostly found where their side chains can fit nicely into the beta configuration. The structure of polypeptide main chains is mostly of hydrogen-bonding; each residue has a carbonyl group that is a good hydrogen- bond acceptor; nitrogen- hydrogen group, a good hydrogen- bond donor. Alpha helix look like the outside of structure. + Right hand appeared in right bottom of Rachamanda plot often + Left hand (LOOP): rare on the left top of Ramacha plot [edit]Alpha Helix [edit]Structure The general physical properties of an alpha helix are: Alpha helix project outward in helical array Ribbon displaying the backbone of the alpha helix 3.6 residues per turn Translation (rise) of 1.5 A Rotation of 100 degrees Pitch (or height) of 5.4A (1.5A*3.6 residues) Alpha helix with hydrogen bonds Screw sense = clockwise (usually) because it would be less sterically hindered Inside the helix consist of the coiled backbone and the side chains project outward in helical array Hydrogen bonding between the 1st carbonyl to the hydrogen on the 5th amino The shorthand drawing of the alpha helix is a ribbon or rod Ribbon shorthand notation for the alpha helix Ramachandran diagram Alpha helix falls within quadrant 1 (left-handed helix) and 3 (right-handed helix) in the Ramachandran diagram [edit]Supersecondary Structure of Alpha Helix [edit]Fibrous Proteins I. COILED-COIL (a-keratin) An alpha coiled coil consists of two or more alpha helices intertwined, creating a stable structure. This structure provides support to tissues and cell, contributing to the cell cytoskeleton and muscle proteins such as myosin and tropomyosin. Alpha keratin consists of heptad repeats (imperfect repeats of 7 amino acid sequences). This facilitates bonding between the two or more helices. II. COLLAGEN Collagen is another type of fibrous protein that consists of three helical polypeptide chains. It is the most abundant protein found in mammals, making up a large component of skin, bone, tendon, cartilage, and teeth. Wrinkles are also caused by the degradations of this protein. In the structure of collagen, every third residue in the polypeptide is glycine because it is the only residue that is small enough to fit in the interior position of the superhelical cable. Unlike normal alpha helices, each collagen helix is stabilized by steric repulsion of the pyrrolidine rings of the praline and hydroxyproline residues. However, the three strands intertwined are stabilized by hydrogen bonding. [edit]Alpha Tertiary I. MOTIFS Motifs are simple combinations of the secondary structure such as the helix-turn-helix, which consist of two helices separated by a turn. The helix-turn-helix motif are usually found in DNA-binding proteins. II. DOMAINS (GLOBULAR) Domains, or compact globulars, consist of multiple motifs.They are polypeptide chains folded into two or more compact regions connected by turns or loops. Their structure is spherical, which is beneficial for the protein because it conserves space. Generally, inside the globular protein consist of hydrophobic amino acids such as leucine, valine, methionine, and phenylalanine. The outside consists of amino acids with hydrophilic tendencies such as aspartate, glutamate, lysine, and arginine. An example of a globular protein is myoglobin, which is the oxygen carrier in muscle. It is an extremely compact molecule made of only alpha helices (70%) except for loops and turns (30%). [edit]Transmembrane and Non-Transmembrane Hydrophobic Helix Studying the topography of transmembrane and non-transmembrane helix have helped answer many questions about membrane protein insertion. Specifically, studying the sequence and lipid dependence of the topography provide insights into post-translational topography changes. Furthermore, studying topography has lead to the design of hydrophobic helices that have biomedical applications. For example, a tumor marker called pHLIP peptide has been designed. Different tests have been used to show the various effects on the