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BIO130H1 (167)

bio lec.3 pg 125-139.docx

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University of Toronto St. George

Proteins: Proteins constitute most of a cells dry mass. Not only are they the building blocks, they also carry out most of the cells functions. Enzymes promote many of the chemical reactions. Proteins embedded in the plasma membrane form channels and pumps that control the passage of small molecules in and out the cell. Other proteins carry messages from one cell to another. Kinesin: protein that propels organelles through cytoplasm. Topoisomerase: protein that untangles knotted DNA molecules. Other specialized proteins act as antibodies, toxins, hormones, antifreeze molecules elastic fibers, ropes or sources of luminescence. Protein: a molecule made up of long chains of amino acids, each linked to its neighbor with a covalent bond. AKA polypeptides. Each protein has its own unique amino acid sequence. Polypeptide backbone: the repeating sequence of atoms along the core of the polypeptide chain. Attached to this repetitive chain are the portions of the amino acids that are NOT involved in making a peptide bond, that give each amino acid its unique properties. * figure 3-1 very important. - Atoms behave almost as if they were hard spheres with a definite radius (their van der Waals forces). The requirement that no two atoms overlap limits the possible bond angles in a polypeptide chain. This constraint and other steric interactions severely restrict the possible three dimensional arrangements of atoms. Nevertheless a long flexible chain such as the protein can still fold in an enormous number of ways. The folding of a protein however I'd constrained by many different sets of weak non covalent bonds that form between one part of the chain and another. These involve atoms in the polypeptide backbone and amino acids. There are three types of weak bonds: hydrogen bonds, van der Waals attraction, and electrostatic attraction. Many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly together. The (combined strength) of large numbers of no covalent bonds determines the stability of each folded shape. Fig. 3-4 there's a fourth weak force that also helps determine the shape of a protein. Hydrophobic molecules including the non polar side chains of a particular amino acid tend to be forced together in an aqueous solution environment in order to minimize their disruptive effect on the hydrogen bonded network of water molecules. Therefore, an important factor governing the folding of any protein is the distribution of its polar and nonpolar amino acids. The nonpolar (hydrophobic) side chains in a protein-belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan-tend to cluster in the interior of the molecule (just as hydrophobic oil droplets coalesce in water to form one large droplet). This enables them to avoid contact with the water that surrounds them inside a cell. In contrast, polar groups-such as those belonging to Arginine, glutamine, and histidine-tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules (Figure3-5). Polar amino acids buried within the protein are usually hydrogen bonded to other polar amino acids or to the polypeptide backbone.An amino acid has a carbon, a side chain (R) a carboxyl group a hydrogen and an amino group (NH2). _ R is commonly one of the 20 different side chains. At a ph of 7 both amino and carboxyl groups are ionized. Optical isomers. The (pie) carbon atom is asymmetric, which allows for two mirror images (or stereo-) isomers L and D. Families of amino acids: - the common amino acid are groups according to whether their side chains are, acidic, basic, uncharged polar or nonpolar. These 20 amino acids are given both 3 letter and one letter abbreviations. Ex. Lysine is Lys or K. R group is: (CH2)4NH3. Argine is Arg or R, r group is (CH2)3NHC=H2N+NH2. This group is very basic because positive charges are stabilized by resonance. Histidine is His, or H, R group: CH2CNH=CHNH=HC. These nitrogen’s have a relatively weak affinity for an H+ and or only partially positive at a neutral pH. Pg. 128* and 129 boxes memorize each. Amino acids are commonly joined by an amide linkage. Called a peptide bond. Figure 3-4. Proteins fold into a confirmation of lowest energy. As a result of all these interactions, most proteins have a particular three dimensional shape structure which is determined by the order of the amino acids in its chain. Conformation: folded structure of a polypeptide. The final conformation is one that minimizes its free energy. Amino acids sequence contains all the information needed for specifying the three dimensional shape of a protein. Each protein normally folds up into a sin gle stable conformation. However the conformation changes slightly when the protein interacts with other molecules in the cell. In a living cell proteins called Molecular chaperones often assist in protein folding. Molecular chaperons bind to partly folded polypeptide chains and help the progress along the most energetically favorable folding pathway. Fig. 3-5. Fig 3-6. In crowded conditions of the cytoplasm, the protein chaperones prevent temporarily exposed hydrophobic regions from associating with each other to form protein aggregates. However the final 3 dimensional shape is specified by the amino acid sequence, the chaperones. Simply make the folding process more reliable. Proteins come in a variety of shapes and they are generally between 50 to 2000 amino acids long. Large proteins usually consist of several distinct protein domains-structural units that fold more or less independently of each other. Panel 3-2 (pp. 132-133) presents four different representations of a protein domain called SH2, which has important functions in eukaryotic cells. Constructed from a string of 100 amino acids, the structure is displayed as (A) a polypeptide backbone model, (B) a ribbon model, (C) a wire model that includes the amino acid side chains, and (D) a space-filling model.Each of the three horizontal rows shows the protein in a different orientation, and the image is colored in a way that allows the polypeptide chain to be followed from its N-terminus (purple) to its C-terminus (red). Panel 3 is pages 132-133 -The alpha helix and the beta sheets are common folding patterns. These two patterns are particularly common because they result from hydrogen-bonding between the N-H and
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