Aim: To study different types of models for visualizing molecular structures of biomolecules Theory: Biomolecules are polymers of high molecular weight assembled from rel For example: Proteins are long polymers of amino acids. Some proteins function as enzymes; others serve as structural elements, signal receptors, or transporters that carry specific substances into or out of cells. tNucleic acids such as DNA and RNA, are polymers of nucleotides. They store and transmit genetic information ‘Lipids are esters of glycerol and fatty acid. Lipds serve as structural components of membranes, energyrich fuel stores, pigments, and intracellular signals. ‘Polysaccharides are polymers of simple sugars such 2s glucose, and have two majo functions: as energy yielding fuel stores and as extracellular structural elements with specific binding sites for particular proteins: ly simple monomeric units bifferent models are used to understand the conformation ofa biomolecule, which Is essential fo discuss its function. The spatial arrangement of atoms in a protein is called its conformation “Models used for visualizing molecular structures of biomolecules are: 1. Ball and stick models 2. Space-filling models 3. Ribbon Models © scanned with OKEN Scanner+ all and stick models are three-dimensional models that use balls to spatially represent a ‘molecule, The balls ae the atoms ina molecule and sticks are the bonds between specific atoms + articular atoms are associated with different color, for example, + Carbon-bl + hydrogen-white + Oxygen-red + ‘Nitrogen-blue * Double and triple bonds are usually represented by two or three curved rods. respectively + Ina good model, the angles between the rods should be the same as the angles between the bonds, and the distances between the centers of the spheres should be proportional o the distances between the corresponding atomic nucle Merits ‘A ball-and-stick model can be used to show the structure ofa simple molecule. + This type of model has the advantage of showing how the atoms are connected and how they are arranged in space, including the angles between bonds. Demerit: *+ The major disadvantage of a ball and stick model is that it cannot accurately show the space ‘occupied by a molecule considering the spheres are purposely made smaller in length as. compared to the rods used, to provide a clearer view ofthe atoms and bonds throughout the model oO Ball and stick model showing single bonds with one rad and double, Bond with two rod atoms (wo spheres) © scanned with OKEN ScannerSimilar tothe ball and stick model, the space-filling model is also a method of spatially slsplaying a molecule and its characteristics + Aspace-flling model, also known as a calotte model's a type of 30 molecular model where the atoms are represented by spheres whose rai are proportional to the radi of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei, alin the same scale. ‘Spheres ofciferent colors usually represent atoms of different chemical elements Space-flling calotte models ae also referred to as CPK models after the chemists Robert Corey, Linus Pauling, and Walter Koltun, who developed the modeling concept into a useful form, ‘They are distinguished from other 30 representations, such as the balLand-stic, by the use of the fullsize" space-filling spheres forthe atoms, ‘The atoms in the model are color coded with black=carbon, redzoxygen, white=hydrogen, ‘and blue=nitrogen. 5 ‘Merit ‘They are useful for visualizing the effective shape and relative dimensions of a molecule, and (because of the rotatabilty) the shapes of the surface of the various conformers. ‘The main advantage is that it shows the overlap ofthe electron shells ofthe atoms. | Trree-demensional,space-fling model of i T agomplex molecule, THC, the ative Demerit ae agent in marjuana. (On the ather hand, these models mask the chemical bonds between the atoms and make it dificult to see the structure ofthe molecule that is obscured by the atoms nearest to the viewer in 2 particular pose. This has the disadvantage that tis no longer possible to see the, angles between bonds: ‘Space filing Ball and Stick aes loa aee © scanned with OKEN ScannerRibbon diagrams, are 3D schematic representalions of protein stucture and are one of the most common ‘mathods of protein depiction used today ‘Tho bon depicts the general course and organization of the protein backbone in 3D and serves as a Visual framework for hanging deals of the entire atomic structure, such as the balls forthe oxygen atoms attached to myoglobin's active site inthe adjacent figure. S Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone + acholoas are shown as cotled ribbons or hick tubes, + Bsttands as arrows, and non-tepetiive cols or loops as lias or thin tubes. ‘The direction of the polypepide chain le shown locally by the arrows and may be inaicated overall by @ colour ramp along the length of the rbon, Current molecular graphics programs: PyMOL, Molscript Ribbon diagram of myogiobin ‘bound to haem (sticks) and exygen ‘Secondary structure"? (Fed spheres) (208: MBO) otelces (yfncical spiral ibbens, wit bon plane approximately folovng plane of peptides ‘Arrows wih thickness, abou [Link] 3 hick as they are wi, showing crecion p-stvanes and twist ofthe stand om amino to carboxy end -sheels ae seen as uifled because neighboring srandstist in unison, cF t » Bestrand arrows a yo ribbon ofthe structure of hubby poten (2 1282) aS ‘smcohedloops the bbbyroten EDR: 1082) @ scanned with OKEN ScannerLIPIDS + Three ways to represent the two stereoisomers of glyceraldehyde + The stereoisomers of glyceraldehyde are mirror images of each other show the actual configuration of, molecules. By convention Giycorol and a triacylglycerol. The mixed ‘wiacylglycerol shown here has three diferent fatty acs attached tothe alycerol backbone + Ballandertick models © scanned with OKEN ScannerMYOGLOBIN — - First Globular protein, tertiary str + relatively small oxygen-binding protein of muscle cells. + It both stores oxygen and facilitates oxygen diffusion in rapidly contracting muscle tissue. FIGURE 4-16 Tertiary structure of sperm whale myoglobin. (PDE 1D MBO) The orientation of » sroup ts shown in 0 for the hydrophobic esi tie hire vies ea of eel anal; uP) ANDERE OHA wh al din aid side choi rotcin siete. a) The polypeptide bacthone, shawn in 8 GMO Each ter i sphere encompassing ite van des Wale GGuninnn cra ype kirosced by fone Retest cach biyie. sodln Ti yaahatts tees 2 eats shawn tn Sue, crt ort Tights regions of secondary structure, The e-helical regions are nt re bariad in the the prin. = "FABLE 42 b. Conformation in Some Single-Chain Proteins ; Residues (%)* Protein (total residues) wwe cx Helix 8 Conformation Myoglobin (153) sso 78 ° | @ scanned with OKEN ScannerOther examples of Globular Tertiary proteins Cytochrome ¢ cs es aa 2 ee eee a a cv ered ‘afecieetsi an tears that catalyzes tho hydrolytic lhe panrea into th sal intestine where + Lie meeatehia rie eine mee. cleavage of polysaccharides in the catalyzes the hydrolysis of certain bonds in the | Te acto cminst , Bowe cal walls of ne cari ‘ton acs pee angst oe enntains ssngle polrpetids chain cf, * Fourdisulfde bonds contribute stability to * Like ysoryme, ribonuclease has four dsulfde bonds ie eou is strut berweentoop othe peep chat + One AP ofthe plypentise inns * The eles in long eve in the sid of seth cesente {he molecule, called th active sit wich +The rest af the cytochrome echain contains iis the site of substrate binding (here ‘TABLE 4-2 _ ‘Sacsndinescaalssoiet” bailar) sete. B onamatn Some Sige Chal Pas Resdves ()* Protein (ttl esiues) sam Hele Caoeaon ‘Chymatypsin (247) ™° 34 45 RRborucease 124) "7 26 35 Chwckone c(108) oe 39 ° ‘ysonme 129) me 40 2 Modo ESL gg 78 ° © scanned with OKEN Scanner‘The first oligomeric protein for which the three- dimensional structure was determined was hemoglobin, It contains four polypeptide chains (subunits); two identical a chains (141 residues each) and two identical 6 chains (146 residues each) All four chains are held together by noncovalent interactions Each a subunit is paired with a 6 subunit so that, hemoglobin can be considered either a tetramer of four polypeptide subunits or a'dimer of a8 protomers ‘The subunits of hemoglobin are arranged in symmetric pairs, each pair having one a and one 8 subunit. In addition to four polypeptide chains it also has four heme prosthetic groups, in which the iron atoms are in the ferrous (Fe2) state. Hemoglobin is four times as large as myoglobin FIGURE 4-23 Quaternary structure of deoxyhemaglbin. (PDB 1D 218) Xeray difaction analysis of deosyhemoglebin (hemoglobin "without oxygen molecules bound tothe heme groups) shows how the four polypeptide subunits are packed together. (a) ibbon reser tation (b) Aspacetiing model The a subunits are shown in gay and light blue; the 8 subunits in pink and dak blue. Note thatthe heme _70ups Ueda relatively far apa. © scanned with OKEN ScannerDNA Doble Helix cof Phosphors Pei Carbon inthe supe posphate Major « Length] roove 12A 3A Le J A Minor groove 6A 6 5 Width 208 C Space-filling FIGURE 8-15. Watson-Crick model for the structure of DNA. The Criginal model proposed by Watson and Crick had 10 base pairs, of Pyrimidines Purine 34.4 (3.4 nm), por tum ofthe helix: subsequent measurements re 1055 base pairs, oF 36 A (3.6 nm), per turn. @) tation, showing dimensions of the helix. @) Stick 1 Ing the backbone and stacking of the bases. (¢) Space-tling model. © scanned with OKEN ScannerDirection of helix Alom Blom lam ‘gh handed Rgh handed Let hands ~26A ~20A ~iBA septs poral tun n 105 12 _Heli rise per base 26h 34h 37k FIGURE 8-19 Comparison of A,B, and Z forms of DNA. Each tuc- ture shown here has 36 base pais. The bases are shown in gray, the phosphate aloms in yellow, and the riboses and phosphate oxygens inblue, Blue is he color used to represent DNA strands in later chap- lets. The lable summarizes some properties o the three forms of DNA. (a) Aform (b) Bform (c) Zform @ scanned with OKEN ScannerSpace-filling model of RNA Three-dimensional structure of stranded RNA. The bases are shown in gray, the te aloms in phenylalanine tRNA of yeast. yellow, and the riboses and phosphate oxygens in green. Green is used FIGURE 8-25 Typical_right-handed_stacking pattern _of_single- © scanned with OKEN Scanner