[{"Name":"Primary Structure","TopicPlaylistFirstVideoID":0,"Duration":null,"Videos":[{"Watched":false,"Name":"Intro to Protein Structure","Duration":"5m 24s","ChapterTopicVideoID":28338,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":"https://www.proprep.uk/Images/Videos_Thumbnails/28338.jpeg","UploadDate":"2022-01-10T16:28:49.1130000","DurationForVideoObject":"PT5M24S","Description":null,"MetaTitle":"Intro to Protein Structure: Video + Workbook | Proprep","MetaDescription":"Protein\u0027s Three Dimensional Structure - Primary Structure. Watch the video made by an expert in the field. Download the workbook and maximize your learning.","Canonical":"https://www.proprep.uk/general-modules/all/biochemistry/protein%27s-three-dimensional-structure/primary-structure/vid29554","VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.850","Text":"Welcome to the chapter on protein structure."},{"Start":"00:02.850 ","End":"00:05.820","Text":"We\u0027re going to start with an introduction to protein structure,"},{"Start":"00:05.820 ","End":"00:09.315","Text":"where we will introduce the general protein structure and its significance"},{"Start":"00:09.315 ","End":"00:13.140","Text":"and the 4 common levels of structural complexity that are used to define proteins."},{"Start":"00:13.140 ","End":"00:17.535","Text":"What is the most obvious defining factor that distinguishes proteins,"},{"Start":"00:17.535 ","End":"00:19.830","Text":"makes 1 protein an enzyme, another hormone,"},{"Start":"00:19.830 ","End":"00:22.410","Text":"another structural protein, and still another an antibody."},{"Start":"00:22.410 ","End":"00:25.395","Text":"How do they differ chemically is structural."},{"Start":"00:25.395 ","End":"00:28.830","Text":"We will now dive into the world of protein structure."},{"Start":"00:28.830 ","End":"00:31.560","Text":"There are several levels of protein structure."},{"Start":"00:31.560 ","End":"00:34.470","Text":"For large macromolecules such as proteins,"},{"Start":"00:34.470 ","End":"00:37.620","Text":"the structure is described and understood in several levels of"},{"Start":"00:37.620 ","End":"00:41.430","Text":"complexity arranged in a conceptual hierarchy."},{"Start":"00:41.430 ","End":"00:45.265","Text":"4 levels of protein structure are commonly defined as seen here."},{"Start":"00:45.265 ","End":"00:47.570","Text":"A description of all covalent bonds,"},{"Start":"00:47.570 ","End":"00:50.000","Text":"mainly peptide bonds or disulfide bonds linking"},{"Start":"00:50.000 ","End":"00:54.275","Text":"amino acid residues in a polypeptide chain is its primary structure."},{"Start":"00:54.275 ","End":"00:56.060","Text":"You see here it\u0027s the sequence of"},{"Start":"00:56.060 ","End":"00:59.285","Text":"amino acid residues that is considered the primary structure."},{"Start":"00:59.285 ","End":"01:03.425","Text":"The most important element of primary structure is the sequence of amino acid residues."},{"Start":"01:03.425 ","End":"01:07.820","Text":"Secondary structure refers particularly to stable arrangements"},{"Start":"01:07.820 ","End":"01:12.470","Text":"of amino acid residues giving rise to recurring structural patterns."},{"Start":"01:12.470 ","End":"01:19.715","Text":"Protein secondary structure is the 3-dimensional form of local segments of proteins."},{"Start":"01:19.715 ","End":"01:23.540","Text":"The 2 most common secondary structural elements are Alpha helices"},{"Start":"01:23.540 ","End":"01:27.720","Text":"as seen here and Beta sheets as seen here."},{"Start":"01:27.720 ","End":"01:30.815","Text":"Though Beta turns and Omega loops occur as well."},{"Start":"01:30.815 ","End":"01:36.350","Text":"Tertiary structure describes all aspects of a 3-dimensional folding of a polypeptide,"},{"Start":"01:36.350 ","End":"01:39.800","Text":"and it is determined by a variety of chemical interactions."},{"Start":"01:39.800 ","End":"01:41.390","Text":"Here you see the primary structure,"},{"Start":"01:41.390 ","End":"01:43.280","Text":"the chain of amino acid,"},{"Start":"01:43.280 ","End":"01:48.330","Text":"as it has folded in a secondary structure."},{"Start":"01:48.330 ","End":"01:52.430","Text":"The tertiary structure is determined by a variety of chemical interactions,"},{"Start":"01:52.430 ","End":"01:56.810","Text":"including hydrophobic interactions, ionic bonding,"},{"Start":"01:56.810 ","End":"01:59.315","Text":"hydrogen bonding seen here,"},{"Start":"01:59.315 ","End":"02:01.805","Text":"and disulfide linkages as seen here."},{"Start":"02:01.805 ","End":"02:06.080","Text":"The 4th level of protein structure is when a protein has"},{"Start":"02:06.080 ","End":"02:09.020","Text":"2 or more polypeptide subunits and"},{"Start":"02:09.020 ","End":"02:13.070","Text":"their arrangement in space is referred to as quaternary structure."},{"Start":"02:13.070 ","End":"02:19.940","Text":"We have the tertiary structure represented in this folding of the chain and this is"},{"Start":"02:19.940 ","End":"02:23.315","Text":"1 polypeptide chain that is arranged"},{"Start":"02:23.315 ","End":"02:27.305","Text":"along with other polypeptide chains in this quaternary structure."},{"Start":"02:27.305 ","End":"02:31.865","Text":"Now you see the box is around this polypeptide chain."},{"Start":"02:31.865 ","End":"02:35.810","Text":"There actually is another similar polypeptide chain arranged in"},{"Start":"02:35.810 ","End":"02:40.670","Text":"a different orientation along with this pink polypeptide chain."},{"Start":"02:40.670 ","End":"02:43.880","Text":"This may be even 2 of them altogether."},{"Start":"02:43.880 ","End":"02:48.070","Text":"These are the assembled subunits that form the quaternary structure."},{"Start":"02:48.070 ","End":"02:52.160","Text":"Just to reiterate, the primary structure consists of a sequence of"},{"Start":"02:52.160 ","End":"02:57.230","Text":"amino acids linked together by peptide bonds and includes any disulfide bonds."},{"Start":"02:57.230 ","End":"03:01.190","Text":"The resulting polypeptide can be coiled into"},{"Start":"03:01.190 ","End":"03:06.260","Text":"units of secondary structure such as an Alpha helix seen here."},{"Start":"03:06.260 ","End":"03:09.380","Text":"This box you see is incorporated,"},{"Start":"03:09.380 ","End":"03:14.900","Text":"it is part of the tertiary structure of the folded polypeptide,"},{"Start":"03:14.900 ","End":"03:16.814","Text":"which is itself,"},{"Start":"03:16.814 ","End":"03:18.110","Text":"this entire thing,"},{"Start":"03:18.110 ","End":"03:21.270","Text":"is one of the subunits that make up"},{"Start":"03:21.270 ","End":"03:25.655","Text":"the quaternary structure of the multi subunit protein."},{"Start":"03:25.655 ","End":"03:29.900","Text":"In this case, what is seen here is hemoglobin."},{"Start":"03:29.900 ","End":"03:33.890","Text":"Now this is to show another representation of"},{"Start":"03:33.890 ","End":"03:40.515","Text":"a quaternary structure because you see multiple subunits arranged together."},{"Start":"03:40.515 ","End":"03:44.509","Text":"Let\u0027s go at this, a different illustration just to visualize,"},{"Start":"03:44.509 ","End":"03:47.180","Text":"maybe this will be easier to understand at home."},{"Start":"03:47.180 ","End":"03:48.770","Text":"You have a primary structure,"},{"Start":"03:48.770 ","End":"03:51.650","Text":"which is the amino acid residues,"},{"Start":"03:51.650 ","End":"03:52.985","Text":"the chain of them."},{"Start":"03:52.985 ","End":"03:57.410","Text":"You have a secondary structure which refers to the stable arrangement with"},{"Start":"03:57.410 ","End":"04:03.600","Text":"Alpha helices being 1 example and Beta sheets being another example."},{"Start":"04:03.600 ","End":"04:06.620","Text":"The tertiary structure is how these aspects"},{"Start":"04:06.620 ","End":"04:09.620","Text":"of the 3-dimensional folding of a polypeptide are"},{"Start":"04:09.620 ","End":"04:15.665","Text":"arranged with the multiple subunits are what define the quaternary structure."},{"Start":"04:15.665 ","End":"04:18.695","Text":"Differences in primary structure are quite informative."},{"Start":"04:18.695 ","End":"04:22.925","Text":"Each protein has a distinctive number and sequence of amino acid residues."},{"Start":"04:22.925 ","End":"04:25.430","Text":"The primary structure of a protein determines how it folds"},{"Start":"04:25.430 ","End":"04:27.845","Text":"up into its unique 3-dimensional structure,"},{"Start":"04:27.845 ","End":"04:35.350","Text":"which you can also see written as 3D structure or 3-dimensional structure."},{"Start":"04:35.350 ","End":"04:40.040","Text":"This 3-dimensional structure in turn determines the function of the protein."},{"Start":"04:40.040 ","End":"04:43.220","Text":"This is what links amino acid sequence and protein function,"},{"Start":"04:43.220 ","End":"04:45.550","Text":"and we\u0027ll talk about this in the next lesson."},{"Start":"04:45.550 ","End":"04:48.710","Text":"The simple string of letters denoting the amino acid sequence of"},{"Start":"04:48.710 ","End":"04:53.000","Text":"a given protein misrepresents the wealth of information the sequence holds."},{"Start":"04:53.000 ","End":"04:55.440","Text":"As more protein sequence have become available,"},{"Start":"04:55.440 ","End":"04:57.860","Text":"the development of more powerful methods for extracting"},{"Start":"04:57.860 ","End":"05:01.085","Text":"information from them has become a major biochemical enterprise."},{"Start":"05:01.085 ","End":"05:05.495","Text":"Each protein\u0027s function relies on its 3-dimensional structure."},{"Start":"05:05.495 ","End":"05:09.500","Text":"Protein sequences are also giving us a window"},{"Start":"05:09.500 ","End":"05:13.880","Text":"into how the proteins evolved and ultimately how life evolved."},{"Start":"05:13.880 ","End":"05:16.730","Text":"This week covered the introduction to protein structure,"},{"Start":"05:16.730 ","End":"05:19.700","Text":"where we talked about the general protein structure and its significance and"},{"Start":"05:19.700 ","End":"05:24.779","Text":"the 4 common levels of structure complexity that are used to define proteins."}],"ID":29554},{"Watched":false,"Name":"Exercise 1","Duration":"1m 9s","ChapterTopicVideoID":28339,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.360","Text":"Hi there. We\u0027re in the chapter of protein structure."},{"Start":"00:03.360 ","End":"00:06.165","Text":"We just covered Intro to Protein Structure."},{"Start":"00:06.165 ","End":"00:07.905","Text":"Let\u0027s test our knowledge."},{"Start":"00:07.905 ","End":"00:11.190","Text":"What is the defining factor that distinguishes proteins,"},{"Start":"00:11.190 ","End":"00:13.200","Text":"makes 1 protein an enzyme, another hormone,"},{"Start":"00:13.200 ","End":"00:16.020","Text":"et cetera, and how do they differ chemically?"},{"Start":"00:16.020 ","End":"00:19.740","Text":"The defining factor that distinguishes proteins is structural."},{"Start":"00:19.740 ","End":"00:22.470","Text":"There are several levels of protein structure."},{"Start":"00:22.470 ","End":"00:27.450","Text":"For proteins, the structure is described and understood in several levels of complexity."},{"Start":"00:27.450 ","End":"00:31.100","Text":"Commonly, 4 levels of protein structure are defined."},{"Start":"00:31.100 ","End":"00:33.290","Text":"Here you see the 4 common levels."},{"Start":"00:33.290 ","End":"00:35.375","Text":"The first level is primary structure."},{"Start":"00:35.375 ","End":"00:38.450","Text":"This is the sequence of amino acid residues."},{"Start":"00:38.450 ","End":"00:42.875","Text":"The secondary structure is how these amino acid residues arrange."},{"Start":"00:42.875 ","End":"00:46.820","Text":"Tertiary structure is how the polypeptide chain folds and quaternary"},{"Start":"00:46.820 ","End":"00:51.559","Text":"structure is how multiple subunits come together and arrange."},{"Start":"00:51.559 ","End":"00:55.887","Text":"Each protein has a distinctive number and sequence of amino acid residues,"},{"Start":"00:55.887 ","End":"00:58.190","Text":"while the primary structure of a protein determines how it"},{"Start":"00:58.190 ","End":"01:01.100","Text":"folds up into its unique 3-dimensional structure,"},{"Start":"01:01.100 ","End":"01:03.905","Text":"and this in turn determines the function of the protein."},{"Start":"01:03.905 ","End":"01:09.120","Text":"Finally, this is what links amino acid sequence and protein function."}],"ID":29555},{"Watched":false,"Name":"Exercise 2","Duration":"1m 44s","ChapterTopicVideoID":28340,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.185","Text":"Welcome to another exercise within the introduction to protein structure."},{"Start":"00:04.185 ","End":"00:06.660","Text":"We introduced several levels of protein structure."},{"Start":"00:06.660 ","End":"00:09.090","Text":"Since large macromolecules, such as proteins,"},{"Start":"00:09.090 ","End":"00:10.980","Text":"have several levels of complexity,"},{"Start":"00:10.980 ","End":"00:13.740","Text":"and these are arranged in a conceptual hierarchy."},{"Start":"00:13.740 ","End":"00:17.295","Text":"Please mention how many and what each one of them is."},{"Start":"00:17.295 ","End":"00:20.550","Text":"There are 4 levels of protein structure which are commonly defined."},{"Start":"00:20.550 ","End":"00:22.290","Text":"You see the 4 here, primary,"},{"Start":"00:22.290 ","End":"00:24.825","Text":"secondary, tertiary, and quaternary."},{"Start":"00:24.825 ","End":"00:27.690","Text":"Covalent bonds, mainly peptide bonds,"},{"Start":"00:27.690 ","End":"00:30.120","Text":"the disulfide bonds linking amino acid residues in"},{"Start":"00:30.120 ","End":"00:33.105","Text":"a polypeptide chain is its primary structure."},{"Start":"00:33.105 ","End":"00:37.715","Text":"The most important element of primary structure is the sequence of amino acid residues."},{"Start":"00:37.715 ","End":"00:40.100","Text":"Secondary structure refers to a stable arrangement of"},{"Start":"00:40.100 ","End":"00:43.609","Text":"amino acid residues giving rise to recurring structural patterns."},{"Start":"00:43.609 ","End":"00:48.515","Text":"Protein\u0027s secondary structure is the 3-dimensional form of local segments of proteins."},{"Start":"00:48.515 ","End":"00:55.305","Text":"The 2 most common secondary structural elements are Alpha helices and Beta sheets."},{"Start":"00:55.305 ","End":"00:58.775","Text":"The Beta turns and Omega loops occur as well."},{"Start":"00:58.775 ","End":"01:02.270","Text":"Tertiary structure describes all aspects of 3-dimensional folding of"},{"Start":"01:02.270 ","End":"01:06.980","Text":"a polypeptide and this is determined by a variety of chemical interactions as seen here,"},{"Start":"01:06.980 ","End":"01:09.160","Text":"disulfide bonds, hydrogen bonding, et cetera."},{"Start":"01:09.160 ","End":"01:11.840","Text":"When a protein has 2 or more polypeptide subunits,"},{"Start":"01:11.840 ","End":"01:15.640","Text":"their arrangement in space is referred to as quaternary structure."},{"Start":"01:15.640 ","End":"01:17.510","Text":"You have primary structure,"},{"Start":"01:17.510 ","End":"01:20.300","Text":"the sequence of amino acid residues,"},{"Start":"01:20.300 ","End":"01:25.730","Text":"the chain secondary structure is the arrangement of these amino acid residues."},{"Start":"01:25.730 ","End":"01:30.755","Text":"Tertiary structure is the folding of itself of the polypeptide chain."},{"Start":"01:30.755 ","End":"01:36.245","Text":"You can see this plays into this and the polypeptide chains tertiary structure"},{"Start":"01:36.245 ","End":"01:38.990","Text":"is part of the quaternary structure where it\u0027s"},{"Start":"01:38.990 ","End":"01:43.050","Text":"the assembly of multiple polypeptide subunits."}],"ID":29556},{"Watched":false,"Name":"Exercise 3","Duration":"36s","ChapterTopicVideoID":28341,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.500","Text":"Welcome back to another exercise in the topic of introduction to protein structure."},{"Start":"00:04.500 ","End":"00:08.189","Text":"Describe how differences in primary structure of proteins are informative."},{"Start":"00:08.189 ","End":"00:11.835","Text":"Differences in primary structure are quite informative in the fact that"},{"Start":"00:11.835 ","End":"00:15.990","Text":"each protein has a distinctive number and sequence of amino acid residues."},{"Start":"00:15.990 ","End":"00:18.360","Text":"The primary structure of a protein determines how it"},{"Start":"00:18.360 ","End":"00:21.165","Text":"folds up into its unique 3-dimensional structure,"},{"Start":"00:21.165 ","End":"00:23.985","Text":"and this in turn determines the function of the protein,"},{"Start":"00:23.985 ","End":"00:27.420","Text":"which is what links amino acid sequence and protein function."},{"Start":"00:27.420 ","End":"00:30.945","Text":"Protein sequences are also giving us a window into how"},{"Start":"00:30.945 ","End":"00:36.370","Text":"the proteins evolved and ultimately how life evolved on this planet."}],"ID":29557},{"Watched":false,"Name":"Protein Function and Structure","Duration":"3m 40s","ChapterTopicVideoID":28342,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.180","Text":"Welcome to the second topic within protein structure,"},{"Start":"00:03.180 ","End":"00:05.865","Text":"we are talking about protein function and structure."},{"Start":"00:05.865 ","End":"00:08.460","Text":"By the end of this section you will be able to talk about the themes of"},{"Start":"00:08.460 ","End":"00:12.435","Text":"protein structure and the term conformation and its significance."},{"Start":"00:12.435 ","End":"00:14.415","Text":"Let\u0027s start with some basics."},{"Start":"00:14.415 ","End":"00:19.695","Text":"The covalent backbone of a typical protein contains hundreds of bonds."},{"Start":"00:19.695 ","End":"00:22.485","Text":"Free rotation as possible around many of these bonds,"},{"Start":"00:22.485 ","End":"00:26.090","Text":"the protein can assume an unlimited number of conformations."},{"Start":"00:26.090 ","End":"00:29.780","Text":"Consider however each protein has a specific chemical or"},{"Start":"00:29.780 ","End":"00:34.880","Text":"structural function strongly suggesting a unique 3-dimensional structure."},{"Start":"00:34.880 ","End":"00:37.940","Text":"We will explore the 3-dimensional structure of proteins,"},{"Start":"00:37.940 ","End":"00:41.075","Text":"emphasizing 5 themes of protein structure."},{"Start":"00:41.075 ","End":"00:44.540","Text":"First, the 3-dimensional structure of a protein is determined"},{"Start":"00:44.540 ","End":"00:48.140","Text":"by its amino acid sequence going back to the primary structure."},{"Start":"00:48.140 ","End":"00:52.380","Text":"Second, the function of a protein depends on its structure,"},{"Start":"00:52.380 ","End":"00:56.495","Text":"and this can mean any part of these because these all affect each other."},{"Start":"00:56.495 ","End":"00:59.090","Text":"Third, an isolated protein usually exists in"},{"Start":"00:59.090 ","End":"01:02.920","Text":"1 or a small number of stable structural forms."},{"Start":"01:02.920 ","End":"01:07.040","Text":"Fourth, the most important forces stabilizing"},{"Start":"01:07.040 ","End":"01:13.175","Text":"the specific structures maintained by a given protein are non-covalent interactions,"},{"Start":"01:13.175 ","End":"01:17.020","Text":"so you have hydrogen bonding, disulfide bonds, etc."},{"Start":"01:17.020 ","End":"01:21.830","Text":"Finally, fifth, amidst the huge number of unique protein structures,"},{"Start":"01:21.830 ","End":"01:25.010","Text":"we can recognize some common structural patterns that help"},{"Start":"01:25.010 ","End":"01:28.340","Text":"us organize our understanding of protein architecture."},{"Start":"01:28.340 ","End":"01:30.620","Text":"These themes should not be taken to imply that"},{"Start":"01:30.620 ","End":"01:34.250","Text":"proteins have static unchanging 3-dimensional structures."},{"Start":"01:34.250 ","End":"01:40.160","Text":"Protein function often entails an interconversion between 2 or more structural forms."},{"Start":"01:40.160 ","End":"01:42.630","Text":"We know that protein structure is actually dynamic,"},{"Start":"01:42.630 ","End":"01:45.320","Text":"and we have previously established there\u0027s a relationship between"},{"Start":"01:45.320 ","End":"01:50.065","Text":"the amino acid sequence of a protein and its 3-dimensional structure and it is complex."},{"Start":"01:50.065 ","End":"01:56.080","Text":"An understanding of protein structure is essential to the discussion of function."},{"Start":"01:56.080 ","End":"01:59.585","Text":"Let\u0027s take a step back and introduce the basics of protein structure."},{"Start":"01:59.585 ","End":"02:03.950","Text":"The spatial arrangement of atoms in a protein is called its conformation."},{"Start":"02:03.950 ","End":"02:06.605","Text":"The possible conformations of proteins include"},{"Start":"02:06.605 ","End":"02:11.915","Text":"any structural state that can be achieved without breaking covalent bonds."},{"Start":"02:11.915 ","End":"02:17.185","Text":"A change in conformation could occur for example by rotation around single bonds."},{"Start":"02:17.185 ","End":"02:20.090","Text":"Of the numerous conformations that are theoretically possible"},{"Start":"02:20.090 ","End":"02:23.180","Text":"in a protein containing hundreds of single bonds,"},{"Start":"02:23.180 ","End":"02:25.160","Text":"1 or more commonly,"},{"Start":"02:25.160 ","End":"02:29.675","Text":"a few conformations generally predominate under biological conditions,"},{"Start":"02:29.675 ","End":"02:32.840","Text":"meaning there are just a few conformations that are"},{"Start":"02:32.840 ","End":"02:37.025","Text":"found commonly in nature for each specific protein."},{"Start":"02:37.025 ","End":"02:41.300","Text":"The presence of multiple stable conformations reflects the changes that"},{"Start":"02:41.300 ","End":"02:45.620","Text":"must occur in most proteins as they bind to other molecules or catalyzed reactions."},{"Start":"02:45.620 ","End":"02:48.680","Text":"If we\u0027re talking about an enzyme, the conformation,"},{"Start":"02:48.680 ","End":"02:53.705","Text":"how to adjust affects what actual substrate can fit"},{"Start":"02:53.705 ","End":"03:00.575","Text":"and be catalyzed or part of reaction that this enzyme is involved in."},{"Start":"03:00.575 ","End":"03:04.400","Text":"The conformations existing under a given set of"},{"Start":"03:04.400 ","End":"03:10.070","Text":"conditions are usually the ones that are thermodynamically the most stable,"},{"Start":"03:10.070 ","End":"03:13.510","Text":"having the lowest Gibbs free energy,"},{"Start":"03:13.510 ","End":"03:21.080","Text":"G. Proteins and any other functional folded conformations are called native proteins."},{"Start":"03:21.080 ","End":"03:24.770","Text":"What principles determine the most stable conformations of a protein?"},{"Start":"03:24.770 ","End":"03:29.290","Text":"We\u0027ll get into that in the following lesson by introducing some guiding principles."},{"Start":"03:29.290 ","End":"03:31.580","Text":"With that, we completed protein function and"},{"Start":"03:31.580 ","End":"03:34.250","Text":"structure within the chapter of protein structure,"},{"Start":"03:34.250 ","End":"03:37.040","Text":"and we covered the themes of protein structure and"},{"Start":"03:37.040 ","End":"03:40.710","Text":"the term conformation and its significance."}],"ID":29558},{"Watched":false,"Name":"Exercise 4","Duration":"45s","ChapterTopicVideoID":28343,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.695","Text":"Welcome to an exercise on protein function and structure."},{"Start":"00:04.695 ","End":"00:06.480","Text":"Protein structure is dynamic,"},{"Start":"00:06.480 ","End":"00:09.330","Text":"explain what this means and its significance."},{"Start":"00:09.330 ","End":"00:14.880","Text":"The covalent backbone of a typical protein contains hundreds of individual bonds."},{"Start":"00:14.880 ","End":"00:18.260","Text":"Free rotation is possible around many of these bonds,"},{"Start":"00:18.260 ","End":"00:22.575","Text":"thus the protein can assume an unlimited number of conformations."},{"Start":"00:22.575 ","End":"00:27.795","Text":"Protein function often entails an interconversion between 2 or more structural forms."},{"Start":"00:27.795 ","End":"00:29.930","Text":"Of the numerous conformations that are theoretically"},{"Start":"00:29.930 ","End":"00:32.765","Text":"possible in a protein containing hundreds of single bonds,"},{"Start":"00:32.765 ","End":"00:37.910","Text":"1 or more commonly a few confirmations generally predominate under biological conditions,"},{"Start":"00:37.910 ","End":"00:40.340","Text":"reflecting that these play a role in function,"},{"Start":"00:40.340 ","End":"00:44.250","Text":"binding other molecules or catalysis or reactions."}],"ID":29559},{"Watched":false,"Name":"Exercise 5","Duration":"1m 51s","ChapterTopicVideoID":28326,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.590","Text":"We are in an exercise within protein function and structure."},{"Start":"00:04.590 ","End":"00:08.655","Text":"What are the 5 themes of protein structure as explained in the lesson?"},{"Start":"00:08.655 ","End":"00:11.655","Text":"The 5 themes of protein structure are 1,"},{"Start":"00:11.655 ","End":"00:15.630","Text":"the 3-dimensional structure of a protein is determined by its amino acid sequence."},{"Start":"00:15.630 ","End":"00:19.770","Text":"This sequence affects how it actually folds upon itself."},{"Start":"00:19.770 ","End":"00:21.885","Text":"Here we see Alpha helices, Beta sheets."},{"Start":"00:21.885 ","End":"00:23.490","Text":"This is the amino acid sequence,"},{"Start":"00:23.490 ","End":"00:25.695","Text":"it affects the secondary structure."},{"Start":"00:25.695 ","End":"00:28.170","Text":"It is what allows for this deform we see here."},{"Start":"00:28.170 ","End":"00:32.365","Text":"Again, an Alpha helix both of these are examples"},{"Start":"00:32.365 ","End":"00:37.880","Text":"of the Alpha helix and how this is part of the tertiary structure,"},{"Start":"00:37.880 ","End":"00:41.900","Text":"meaning this all goes back to this primary structure,"},{"Start":"00:41.900 ","End":"00:43.655","Text":"the sequence of amino acids."},{"Start":"00:43.655 ","End":"00:46.895","Text":"Now the function of a protein depends on its structure as well,"},{"Start":"00:46.895 ","End":"00:51.130","Text":"how this assembles into the actual quaternary structure."},{"Start":"00:51.130 ","End":"00:55.565","Text":"For example, where there are multiple sub-units or even just this structure right here,"},{"Start":"00:55.565 ","End":"00:59.450","Text":"affects the protein\u0027s ability to function and how it functions."},{"Start":"00:59.450 ","End":"01:04.460","Text":"An isolated protein usually exist in 1 or a small number of stable structural forms."},{"Start":"01:04.460 ","End":"01:07.190","Text":"The most important forces stabilizing the specific structures"},{"Start":"01:07.190 ","End":"01:10.070","Text":"maintained by a given protein are non-covalent interactions."},{"Start":"01:10.070 ","End":"01:11.885","Text":"We mentioned hydrogen bonding,"},{"Start":"01:11.885 ","End":"01:13.540","Text":"disulfide bonds, et cetera."},{"Start":"01:13.540 ","End":"01:15.800","Text":"Among the huge number of unique protein structures,"},{"Start":"01:15.800 ","End":"01:18.545","Text":"we recognize some common structural patterns that help"},{"Start":"01:18.545 ","End":"01:21.620","Text":"organize our understanding of protein architecture."},{"Start":"01:21.620 ","End":"01:24.465","Text":"These are the 5 themes of protein structure."},{"Start":"01:24.465 ","End":"01:27.635","Text":"The 3-dimensional structure determined by its amino acid sequence,"},{"Start":"01:27.635 ","End":"01:29.945","Text":"function depends on structure,"},{"Start":"01:29.945 ","End":"01:34.605","Text":"proteins usually exist in a small number of stable structural forms,"},{"Start":"01:34.605 ","End":"01:36.380","Text":"the most important force stabilizing"},{"Start":"01:36.380 ","End":"01:39.995","Text":"the specific structures are non-covalent interactions."},{"Start":"01:39.995 ","End":"01:43.429","Text":"Within the unique protein structures they are generally"},{"Start":"01:43.429 ","End":"01:45.950","Text":"some common structural patterns that help"},{"Start":"01:45.950 ","End":"01:50.129","Text":"us recognize and understand protein architecture."}],"ID":29560},{"Watched":false,"Name":"Exercise 6","Duration":"1m 3s","ChapterTopicVideoID":28327,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.765","Text":"Welcome back to another exercise on protein function and structure."},{"Start":"00:03.765 ","End":"00:07.410","Text":"What is a native conformation, a native protein?"},{"Start":"00:07.410 ","End":"00:11.880","Text":"The spatial arrangement of atoms in a protein is called its conformation."},{"Start":"00:11.880 ","End":"00:15.000","Text":"Of the numerous conformations that are theoretically possible in"},{"Start":"00:15.000 ","End":"00:18.120","Text":"a protein containing hundreds of single bonds,"},{"Start":"00:18.120 ","End":"00:23.393","Text":"1 or a few conformations generally predominate under biological conditions,"},{"Start":"00:23.393 ","End":"00:24.930","Text":"so there are many options that can be"},{"Start":"00:24.930 ","End":"00:27.795","Text":"predicted if we look at sequence or protein behavior,"},{"Start":"00:27.795 ","End":"00:32.220","Text":"still there are only a few conformations that are generally found under"},{"Start":"00:32.220 ","End":"00:38.130","Text":"biological conditions in nature and this reflects that these play a role in function,"},{"Start":"00:38.130 ","End":"00:41.300","Text":"binding other molecules or catalysis or reactions."},{"Start":"00:41.300 ","End":"00:46.835","Text":"Proteins in their functional folded conformations are called native proteins."},{"Start":"00:46.835 ","End":"00:49.940","Text":"What you see here is an example,"},{"Start":"00:49.940 ","End":"00:52.730","Text":"an illustration representing hemoglobin,"},{"Start":"00:52.730 ","End":"00:57.710","Text":"and this is how it is found most commonly in nature."},{"Start":"00:57.710 ","End":"01:02.070","Text":"Biologically, this is the native protein."}],"ID":29561},{"Watched":false,"Name":"Protein Conformations Part 1","Duration":"9m 45s","ChapterTopicVideoID":28328,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.440","Text":"Let\u0027s talk about protein conformations within protein structures."},{"Start":"00:04.440 ","End":"00:06.930","Text":"By the end of this section, you\u0027ll be able to understand"},{"Start":"00:06.930 ","End":"00:10.860","Text":"protein conformation and comprehend the stabilizing forces of protein conformation."},{"Start":"00:10.860 ","End":"00:12.945","Text":"We\u0027re going to split it into 2 portions."},{"Start":"00:12.945 ","End":"00:15.300","Text":"Let\u0027s jump in to Part 1."},{"Start":"00:15.300 ","End":"00:20.340","Text":"A protein\u0027s conformation is stabilized largely by weak interactions."},{"Start":"00:20.340 ","End":"00:22.485","Text":"In the context of protein structure,"},{"Start":"00:22.485 ","End":"00:27.930","Text":"the term stability can be defined as the tendency to maintain a native conformation."},{"Start":"00:27.930 ","End":"00:31.110","Text":"Native proteins are only slightly stable."},{"Start":"00:31.110 ","End":"00:35.460","Text":"The Delta G separating the folded and unfolded state in typical proteins under"},{"Start":"00:35.460 ","End":"00:40.575","Text":"physiological conditions is in the range of only 20-65 kilojoules per mole,"},{"Start":"00:40.575 ","End":"00:47.764","Text":"meaning it\u0027s a slight change in energy that allows them to shift and change"},{"Start":"00:47.764 ","End":"00:50.045","Text":"quite easily than when there is"},{"Start":"00:50.045 ","End":"00:55.445","Text":"a great energy investment that is required in order to change or maintain forms."},{"Start":"00:55.445 ","End":"01:01.655","Text":"A given polypeptide chain can theoretically assume countless different confirmations,"},{"Start":"01:01.655 ","End":"01:04.040","Text":"and as a result, the unfolded state of"},{"Start":"01:04.040 ","End":"01:07.970","Text":"the protein is characterized by a high degree of conformational entropy."},{"Start":"01:07.970 ","End":"01:10.700","Text":"This entropy in the hydrogen bonding interactions of"},{"Start":"01:10.700 ","End":"01:14.150","Text":"many groups in the polypeptide chain with solvent water,"},{"Start":"01:14.150 ","End":"01:16.595","Text":"tend to maintain the unfolded state."},{"Start":"01:16.595 ","End":"01:19.910","Text":"The chemical interactions that counteract"},{"Start":"01:19.910 ","End":"01:23.240","Text":"these effects and stabilize the native conformation include"},{"Start":"01:23.240 ","End":"01:29.945","Text":"disulfide bonds and the weak non-covalent interactions we described in previous chapter."},{"Start":"01:29.945 ","End":"01:31.820","Text":"This includes hydrogen bonds,"},{"Start":"01:31.820 ","End":"01:34.445","Text":"the hydrophobic effect, and ionic interactions."},{"Start":"01:34.445 ","End":"01:36.275","Text":"Just as an FYI,"},{"Start":"01:36.275 ","End":"01:38.795","Text":"not all proteins have disulfide bonds."},{"Start":"01:38.795 ","End":"01:40.720","Text":"Many proteins do not."},{"Start":"01:40.720 ","End":"01:44.540","Text":"Appreciation of the role of these weak interactions is"},{"Start":"01:44.540 ","End":"01:48.380","Text":"especially important to our understanding of how polypeptide chains"},{"Start":"01:48.380 ","End":"01:51.920","Text":"fold into specific secondary and tertiary structures and how they"},{"Start":"01:51.920 ","End":"01:56.010","Text":"combine with other polypeptides to form quaternary structures."},{"Start":"01:56.010 ","End":"02:02.255","Text":"About 200-460 kilojoules per mole are required to break a single covalent bond,"},{"Start":"02:02.255 ","End":"02:05.065","Text":"whereas weak contractions can be disrupted by"},{"Start":"02:05.065 ","End":"02:08.030","Text":"4-30 kilojoules per mole, as I mentioned before,"},{"Start":"02:08.030 ","End":"02:11.390","Text":"with regard to shifting from native conformation and"},{"Start":"02:11.390 ","End":"02:15.170","Text":"shifting out of that confirmation as not being completely stable,"},{"Start":"02:15.170 ","End":"02:18.064","Text":"so this is a magnitude smaller."},{"Start":"02:18.064 ","End":"02:22.985","Text":"This is way easier to disrupt versus covalent bonds."},{"Start":"02:22.985 ","End":"02:27.665","Text":"Individual covalent bonds that contribute to the native conformation of proteins,"},{"Start":"02:27.665 ","End":"02:30.560","Text":"such as disulfide bonds linking separate parts of"},{"Start":"02:30.560 ","End":"02:35.990","Text":"a single polypeptide chain are clearly much stronger than individual weak interactions."},{"Start":"02:35.990 ","End":"02:38.510","Text":"Yet, because they\u0027re so numerous,"},{"Start":"02:38.510 ","End":"02:42.770","Text":"weak interactions predominate as a stabilizing force in protein structure."},{"Start":"02:42.770 ","End":"02:47.180","Text":"In general, the protein conformation with the lowest free energy,"},{"Start":"02:47.180 ","End":"02:49.790","Text":"that is the most stable conformation,"},{"Start":"02:49.790 ","End":"02:53.125","Text":"is the one with the maximum number of weak interactions."},{"Start":"02:53.125 ","End":"02:58.310","Text":"When evaluating the contribution of weak interactions supporting stability,"},{"Start":"02:58.310 ","End":"03:04.105","Text":"more specifically, it presents that the hydrophobic effect, generally, predominant."},{"Start":"03:04.105 ","End":"03:08.545","Text":"Pure water contains a network of hydrogen-bonded H_2O molecules."},{"Start":"03:08.545 ","End":"03:11.200","Text":"Just reminding you of what we learned in the water chapter,"},{"Start":"03:11.200 ","End":"03:14.230","Text":"no other molecule has the hydrogen bonding potential of water,"},{"Start":"03:14.230 ","End":"03:15.860","Text":"and the presence of other molecules in"},{"Start":"03:15.860 ","End":"03:18.725","Text":"an aqueous solution disrupts the hydrogen bonding of water."},{"Start":"03:18.725 ","End":"03:22.190","Text":"Just a reminder, H_2O, if you have,"},{"Start":"03:22.190 ","End":"03:24.560","Text":"we\u0027ll just color code, H,"},{"Start":"03:24.560 ","End":"03:27.650","Text":"H, H. Here\u0027s 2 molecules."},{"Start":"03:27.650 ","End":"03:30.785","Text":"A quick reminder of hydrogen bonding of H_2O."},{"Start":"03:30.785 ","End":"03:32.015","Text":"This is water molecule,"},{"Start":"03:32.015 ","End":"03:34.295","Text":"there\u0027s 2 hydrogens and 1 oxygen."},{"Start":"03:34.295 ","End":"03:36.905","Text":"The oxygen is bound to the 2 hydrogens."},{"Start":"03:36.905 ","End":"03:39.500","Text":"The hydrogens have a partial positive charge,"},{"Start":"03:39.500 ","End":"03:41.615","Text":"the oxygen has a partial negative charge."},{"Start":"03:41.615 ","End":"03:44.900","Text":"This is what allows hydrogen bonding."},{"Start":"03:44.900 ","End":"03:48.020","Text":"It is a non-covalent weak interaction,"},{"Start":"03:48.020 ","End":"03:52.145","Text":"but it allows this positive and negative to interact."},{"Start":"03:52.145 ","End":"03:54.680","Text":"You can also see this here,"},{"Start":"03:54.680 ","End":"03:57.350","Text":"and this can continue between different molecules."},{"Start":"03:57.350 ","End":"04:01.970","Text":"This hydrogen bond can also interact with a different water molecule that"},{"Start":"04:01.970 ","End":"04:07.250","Text":"sits here where it actually interacts with oxygen in this molecule."},{"Start":"04:07.250 ","End":"04:10.660","Text":"Let\u0027s introduce a term in this regard, solvation layer."},{"Start":"04:10.660 ","End":"04:12.890","Text":"When water surrounds a hydrophobic molecule,"},{"Start":"04:12.890 ","End":"04:15.380","Text":"the optimal arrangement of hydrogen bonds results in"},{"Start":"04:15.380 ","End":"04:18.335","Text":"a highly structured shell, the solvation layer."},{"Start":"04:18.335 ","End":"04:20.360","Text":"Generally defining the term,"},{"Start":"04:20.360 ","End":"04:23.510","Text":"solvation is the process of attraction and association of"},{"Start":"04:23.510 ","End":"04:27.860","Text":"molecules of a solvent with molecules or ions of a solute."},{"Start":"04:27.860 ","End":"04:32.515","Text":"This is also known as a solvation shell or solvation sheath."},{"Start":"04:32.515 ","End":"04:36.695","Text":"What you see here is this solvation shell."},{"Start":"04:36.695 ","End":"04:39.110","Text":"As ions dissolved in a solvent,"},{"Start":"04:39.110 ","End":"04:43.295","Text":"they spread out and become surrounded by solvent molecules."},{"Start":"04:43.295 ","End":"04:44.960","Text":"In the case of an aqueous solution,"},{"Start":"04:44.960 ","End":"04:48.320","Text":"the solute is surrounded by water molecules."},{"Start":"04:48.320 ","End":"04:51.120","Text":"What you see here is a water molecule,"},{"Start":"04:51.120 ","End":"04:52.455","Text":"this is the oxygen,"},{"Start":"04:52.455 ","End":"04:54.485","Text":"and these are the hydrogens."},{"Start":"04:54.485 ","End":"04:57.140","Text":"It\u0027s showing the partial negative charge of"},{"Start":"04:57.140 ","End":"04:59.755","Text":"oxygen and the partial positive charges of hydrogen."},{"Start":"04:59.755 ","End":"05:01.955","Text":"These are water molecules."},{"Start":"05:01.955 ","End":"05:03.260","Text":"When the solvent is water,"},{"Start":"05:03.260 ","End":"05:08.315","Text":"it is often referred to as a hydration shell or a hydration sphere."},{"Start":"05:08.315 ","End":"05:11.585","Text":"The number of solvent molecules surrounding"},{"Start":"05:11.585 ","End":"05:16.625","Text":"each unit of solute is called the hydration number of the solute."},{"Start":"05:16.625 ","End":"05:18.590","Text":"You see the sphere here,"},{"Start":"05:18.590 ","End":"05:22.565","Text":"you see it reversed in the color scheme,"},{"Start":"05:22.565 ","End":"05:24.260","Text":"but you have sodium."},{"Start":"05:24.260 ","End":"05:34.000","Text":"Let\u0027s say, you can just say that this is NaCl that breaks apart Na plus Cl minus,"},{"Start":"05:34.000 ","End":"05:35.655","Text":"just as an example."},{"Start":"05:35.655 ","End":"05:42.170","Text":"This crystalline structure breaks apart because water molecules can come and attract with"},{"Start":"05:42.170 ","End":"05:49.460","Text":"the opposite partial charges and then the water will surround these ions,"},{"Start":"05:49.460 ","End":"05:52.100","Text":"dissolve in the solvent, they spread out,"},{"Start":"05:52.100 ","End":"05:54.620","Text":"and then they become surrounded by the solvent molecules,"},{"Start":"05:54.620 ","End":"05:57.305","Text":"and again, an aqueous solution."},{"Start":"05:57.305 ","End":"05:58.820","Text":"This is water molecules."},{"Start":"05:58.820 ","End":"06:04.670","Text":"The water molecules surround the ion and create a hydration shell."},{"Start":"06:04.670 ","End":"06:08.510","Text":"They\u0027re hydrating and creating a sphere around it."},{"Start":"06:08.510 ","End":"06:12.680","Text":"What you see here is this hydration sphere,"},{"Start":"06:12.680 ","End":"06:14.900","Text":"this thing right here, this circle,"},{"Start":"06:14.900 ","End":"06:16.890","Text":"also known as the hydration shell,"},{"Start":"06:16.890 ","End":"06:18.285","Text":"and you can also see that here,"},{"Start":"06:18.285 ","End":"06:20.143","Text":"this circle that\u0027s created,"},{"Start":"06:20.143 ","End":"06:23.435","Text":"and then the number of these solvent molecules that surrounds"},{"Start":"06:23.435 ","End":"06:26.945","Text":"each unit of solute is called the hydration number of the solute,"},{"Start":"06:26.945 ","End":"06:28.970","Text":"so there will be a typical number."},{"Start":"06:28.970 ","End":"06:30.420","Text":"If we count here 1,"},{"Start":"06:30.420 ","End":"06:32.321","Text":"2, 3, 4, 5,"},{"Start":"06:32.321 ","End":"06:37.010","Text":"6, this will have a hydration number of 6."},{"Start":"06:37.010 ","End":"06:41.525","Text":"A classic example is 1 water molecule is arranged around the metal ion."},{"Start":"06:41.525 ","End":"06:43.220","Text":"If the metal ion is a cation,"},{"Start":"06:43.220 ","End":"06:47.330","Text":"the electronegative oxygen atom of the water molecule is"},{"Start":"06:47.330 ","End":"06:52.340","Text":"attracted electrostatically to the positive charge on the metal ion."},{"Start":"06:52.340 ","End":"06:56.560","Text":"The result is a solvation shell of water molecules that surround the ion,"},{"Start":"06:56.560 ","End":"07:01.325","Text":"and this shell can be several molecules thick dependent upon the charge of the ion,"},{"Start":"07:01.325 ","End":"07:05.215","Text":"its distribution, and spatial dimensions."},{"Start":"07:05.215 ","End":"07:09.950","Text":"The increased order of water molecules in the salvation layer correlates with"},{"Start":"07:09.950 ","End":"07:15.230","Text":"an unfavorable decrease in the entropy or the disorder or randomness of the water."},{"Start":"07:15.230 ","End":"07:17.989","Text":"Yet, when non-polar groups clustered together,"},{"Start":"07:17.989 ","End":"07:22.310","Text":"the extent of the solvation layer decreases because each group no longer presents"},{"Start":"07:22.310 ","End":"07:27.800","Text":"its entire surface to the solution and the result is a favorable increase in entropy."},{"Start":"07:27.800 ","End":"07:32.300","Text":"What does this mean? These individual hydrophobic factors we\u0027ve seen in this figure,"},{"Start":"07:32.300 ","End":"07:36.800","Text":"they arrange together and then now you have them,"},{"Start":"07:36.800 ","End":"07:38.525","Text":"this hydrophobic region,"},{"Start":"07:38.525 ","End":"07:43.685","Text":"they can be closer to each other while the water molecules around it"},{"Start":"07:43.685 ","End":"07:49.340","Text":"are free to move all around it and this gives an increase in entropy,"},{"Start":"07:49.340 ","End":"07:51.830","Text":"and this is always favorable."},{"Start":"07:51.830 ","End":"07:56.950","Text":"There\u0027s always a natural inclination to move towards randomness and disorder."},{"Start":"07:56.950 ","End":"07:59.120","Text":"This increase in entropy and if need be,"},{"Start":"07:59.120 ","End":"08:01.490","Text":"you can refresh these definitions in an earlier chapter,"},{"Start":"08:01.490 ","End":"08:05.525","Text":"is the major thermodynamic driving force"},{"Start":"08:05.525 ","End":"08:10.040","Text":"for the association of hydrophobic groups in aqueous solution."},{"Start":"08:10.040 ","End":"08:12.920","Text":"Hydrophobic amino acid side chains, therefore,"},{"Start":"08:12.920 ","End":"08:16.775","Text":"tend to cluster into proteins interior away from water."},{"Start":"08:16.775 ","End":"08:20.140","Text":"If you look here, remember we talked about the micelle,"},{"Start":"08:20.140 ","End":"08:22.460","Text":"what happens at these side chains,"},{"Start":"08:22.460 ","End":"08:26.420","Text":"the hydrophobic portions, this is the equivalent of these ones."},{"Start":"08:26.420 ","End":"08:27.890","Text":"Also nonpolar."},{"Start":"08:27.890 ","End":"08:34.910","Text":"They cluster together to be away from the aqueous solution that it\u0027s surrounded"},{"Start":"08:34.910 ","End":"08:42.560","Text":"by as to avoid it while the portion that is hydrophilic can interact."},{"Start":"08:42.560 ","End":"08:45.530","Text":"This is what creates many of these structures,"},{"Start":"08:45.530 ","End":"08:47.555","Text":"so the driving force for many of these structures."},{"Start":"08:47.555 ","End":"08:51.055","Text":"Another example is an oil droplet."},{"Start":"08:51.055 ","End":"08:53.060","Text":"You have an oil droplet,"},{"Start":"08:53.060 ","End":"08:55.220","Text":"even though it\u0027s also liquid,"},{"Start":"08:55.220 ","End":"08:57.200","Text":"when it is dropped into water,"},{"Start":"08:57.200 ","End":"09:01.070","Text":"it remains its form because it\u0027s hydrophobic,"},{"Start":"09:01.070 ","End":"09:05.780","Text":"so it\u0027s trying to cluster together as much of the portions of"},{"Start":"09:05.780 ","End":"09:12.240","Text":"the molecules that are hydrophobic in order to avoid the water molecules."},{"Start":"09:12.240 ","End":"09:16.160","Text":"The amino acid sequences of the most proteins, thus,"},{"Start":"09:16.160 ","End":"09:21.875","Text":"include a significant content of hydrophobic amino acids side chains."},{"Start":"09:21.875 ","End":"09:26.525","Text":"These are positions so that they are clustered when the protein is folded,"},{"Start":"09:26.525 ","End":"09:28.910","Text":"forming a hydrophobic protein core."},{"Start":"09:28.910 ","End":"09:32.180","Text":"Under physiological conditions, the formation of hydrogen bonds in"},{"Start":"09:32.180 ","End":"09:36.205","Text":"a protein is driven largely by the same entropic effect."},{"Start":"09:36.205 ","End":"09:39.665","Text":"With that, we concluded Part 1 and talked about"},{"Start":"09:39.665 ","End":"09:45.570","Text":"protein conformations and various stabilizing forces of protein conformation."}],"ID":29562},{"Watched":false,"Name":"Protein Conformations Part 2","Duration":"5m 26s","ChapterTopicVideoID":28329,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.120","Text":"Welcome back to protein conformations, Part II."},{"Start":"00:03.120 ","End":"00:05.685","Text":"We will further talk about protein conformations"},{"Start":"00:05.685 ","End":"00:08.505","Text":"and the various stabilizing forces of protein conformation."},{"Start":"00:08.505 ","End":"00:10.290","Text":"Polar groups can generally form"},{"Start":"00:10.290 ","End":"00:13.410","Text":"hydrogen bonds with water and hence, are soluble in water."},{"Start":"00:13.410 ","End":"00:14.886","Text":"Here to remind you further,"},{"Start":"00:14.886 ","End":"00:17.970","Text":"the number of hydrogen bonds per unit mass is generally"},{"Start":"00:17.970 ","End":"00:21.330","Text":"greater for pure water than for any other liquid or solution and there"},{"Start":"00:21.330 ","End":"00:24.120","Text":"are limits to the solubility of even for"},{"Start":"00:24.120 ","End":"00:26.385","Text":"the most polar molecules as their presence"},{"Start":"00:26.385 ","End":"00:29.535","Text":"causes a net decrease in hydrogen bonding per unit mass."},{"Start":"00:29.535 ","End":"00:32.145","Text":"Therefore, a solvation layer forms to some extent,"},{"Start":"00:32.145 ","End":"00:33.915","Text":"even around polar molecules."},{"Start":"00:33.915 ","End":"00:36.990","Text":"Most of the net change and free energy that occurs when"},{"Start":"00:36.990 ","End":"00:39.950","Text":"contractions are formed within a protein is derived"},{"Start":"00:39.950 ","End":"00:42.460","Text":"from the increased entropy in the surrounding and"},{"Start":"00:42.460 ","End":"00:46.130","Text":"a solution resulting from the burial of hydrophobic surfaces."},{"Start":"00:46.130 ","End":"00:48.710","Text":"This is more than counterbalances the large loss of"},{"Start":"00:48.710 ","End":"00:54.370","Text":"conformational entropy as a polypeptide is constrained into a single folded conformation."},{"Start":"00:54.370 ","End":"01:00.785","Text":"The hydrophobic effect is clearly important in stabilizing protein conformation."},{"Start":"01:00.785 ","End":"01:02.870","Text":"The interior of a protein is generally"},{"Start":"01:02.870 ","End":"01:06.725","Text":"a densely packed core of hydrophobic amino acid side chains."},{"Start":"01:06.725 ","End":"01:11.360","Text":"It is also important that any polar or charged groups in"},{"Start":"01:11.360 ","End":"01:14.000","Text":"the protein interior to have suitable partners"},{"Start":"01:14.000 ","End":"01:16.820","Text":"for hydrogen bonding or ionic interactions."},{"Start":"01:16.820 ","End":"01:21.360","Text":"1 hydrogen bond seems to contribute little to the stability of a native structure,"},{"Start":"01:21.360 ","End":"01:24.050","Text":"but the presence of hydrogen bonding or charged groups"},{"Start":"01:24.050 ","End":"01:27.770","Text":"without partners in the hydrophobic core of a protein can"},{"Start":"01:27.770 ","End":"01:30.980","Text":"be destabilizing that conformations containing"},{"Start":"01:30.980 ","End":"01:34.405","Text":"these groups are often thermodynamically unsustainable."},{"Start":"01:34.405 ","End":"01:35.795","Text":"Just to go back,"},{"Start":"01:35.795 ","End":"01:37.895","Text":"we have polar charged groups."},{"Start":"01:37.895 ","End":"01:40.460","Text":"If they are in the interior,"},{"Start":"01:40.460 ","End":"01:46.490","Text":"it is important for the stability to then have suitable partners for hydrogen bonding or"},{"Start":"01:46.490 ","End":"01:49.670","Text":"ionic interactions to allow this to be"},{"Start":"01:49.670 ","End":"01:53.375","Text":"stable and maintain the structure and the interior."},{"Start":"01:53.375 ","End":"01:55.460","Text":"This is the opposite of what we were talking about,"},{"Start":"01:55.460 ","End":"01:59.210","Text":"what stabilizes the fact that when you have hydrophobic"},{"Start":"01:59.210 ","End":"02:03.535","Text":"or non-polar groups in the interior,"},{"Start":"02:03.535 ","End":"02:06.755","Text":"their repulsion or need to avoid"},{"Start":"02:06.755 ","End":"02:10.460","Text":"water molecule is what keeps them stable on the interior."},{"Start":"02:10.460 ","End":"02:14.570","Text":"The presence of hydrogen bonding or charged groups without partners in"},{"Start":"02:14.570 ","End":"02:17.750","Text":"the hydrophobic core of a protein can be so"},{"Start":"02:17.750 ","End":"02:21.260","Text":"destabilizing that conformations contain these groups are,"},{"Start":"02:21.260 ","End":"02:25.050","Text":"therefore, unsustainable thermodynamically."},{"Start":"02:25.050 ","End":"02:33.110","Text":"The entropy is such that it is not able to maintain the structure in a consistent way."},{"Start":"02:33.110 ","End":"02:38.450","Text":"The favorable free energy change realized by combining such a group with a partner in"},{"Start":"02:38.450 ","End":"02:41.360","Text":"the surrounding solution can be greater than the difference in free energy"},{"Start":"02:41.360 ","End":"02:44.375","Text":"between the folded and unfolded states."},{"Start":"02:44.375 ","End":"02:50.555","Text":"Meaning that this favorable free energy change as having a partner"},{"Start":"02:50.555 ","End":"02:53.660","Text":"will maintain and overcome"},{"Start":"02:53.660 ","End":"02:57.230","Text":"the energy change that is between the folded and unfolded state and,"},{"Start":"02:57.230 ","End":"03:00.320","Text":"therefore, stabilize this structure."},{"Start":"03:00.320 ","End":"03:05.635","Text":"In addition, hydrogen bonds between groups in proteins form cooperatively."},{"Start":"03:05.635 ","End":"03:08.660","Text":"Meaning formation of 1 hydrogen bond"},{"Start":"03:08.660 ","End":"03:12.080","Text":"facilitates the formation of additional hydrogen bond."},{"Start":"03:12.080 ","End":"03:14.090","Text":"In this way, hydrogen bonds often have"},{"Start":"03:14.090 ","End":"03:17.510","Text":"an important role in guiding the protein folding process."},{"Start":"03:17.510 ","End":"03:21.320","Text":"The overall contribution of hydrogen bonds and other non-covalent interactions"},{"Start":"03:21.320 ","End":"03:25.189","Text":"to the stabilization of protein conformation is still being evaluated."},{"Start":"03:25.189 ","End":"03:29.390","Text":"The interaction of oppositely charged groups that form an ion pair of salt bridge may"},{"Start":"03:29.390 ","End":"03:34.235","Text":"also have a stabilizing or destabilizing effect on protein structure."},{"Start":"03:34.235 ","End":"03:37.700","Text":"Ionic interactions also limit structural flexibility and"},{"Start":"03:37.700 ","End":"03:41.480","Text":"convert a uniqueness to a particular protein structure,"},{"Start":"03:41.480 ","End":"03:45.740","Text":"that the clustering of non-polar groups via the hydrophobic effect cannot provide."},{"Start":"03:45.740 ","End":"03:49.440","Text":"In the tightly packed atomic environment of a protein,"},{"Start":"03:49.440 ","End":"03:52.760","Text":"one more type of weak interaction can have an effect,"},{"Start":"03:52.760 ","End":"03:56.375","Text":"and this is a significant effect on protein structure."},{"Start":"03:56.375 ","End":"03:58.670","Text":"This is the Van der Waals interaction."},{"Start":"03:58.670 ","End":"04:02.690","Text":"Another flashback, these are dipole-dipole interactions that provide"},{"Start":"04:02.690 ","End":"04:05.150","Text":"an attractive intermolecular force that operates"},{"Start":"04:05.150 ","End":"04:08.060","Text":"only over a limited intermolecular distance,"},{"Start":"04:08.060 ","End":"04:11.985","Text":"which we measured to be 0.3-0.6 nanometer."},{"Start":"04:11.985 ","End":"04:14.460","Text":"This is a very weak interaction."},{"Start":"04:14.460 ","End":"04:17.420","Text":"In the well pack protein or in an interaction"},{"Start":"04:17.420 ","End":"04:20.649","Text":"between one protein to another protein or other molecule,"},{"Start":"04:20.649 ","End":"04:24.950","Text":"the number of such interactions can be substantial so that"},{"Start":"04:24.950 ","End":"04:32.140","Text":"this weak non-covalent interaction can actually have a significant effect."},{"Start":"04:32.140 ","End":"04:37.759","Text":"Most of the structural patterns we talked about here reflect 2 simple rules."},{"Start":"04:37.759 ","End":"04:44.165","Text":"1, hydrophobic residues are largely buried in a protein interior away from water."},{"Start":"04:44.165 ","End":"04:50.015","Text":"Hydrophobic residues are inside in the protein interior,"},{"Start":"04:50.015 ","End":"04:54.100","Text":"hiding away from water because, remember, phobic."},{"Start":"04:54.100 ","End":"04:57.210","Text":"They don\u0027t like hydro, water."},{"Start":"04:57.210 ","End":"05:02.630","Text":"2, the number of hydrogen bonds within the protein is maximized."},{"Start":"05:02.630 ","End":"05:05.345","Text":"Insoluble proteins and proteins within"},{"Start":"05:05.345 ","End":"05:07.310","Text":"membranes follow somewhat different rules"},{"Start":"05:07.310 ","End":"05:09.590","Text":"because of their function on their environment,"},{"Start":"05:09.590 ","End":"05:13.290","Text":"but weak interactions are still critical structural elements."},{"Start":"05:13.290 ","End":"05:15.560","Text":"We won\u0027t expand on this further here."},{"Start":"05:15.560 ","End":"05:19.770","Text":"With this, we\u0027ve completed protein conformations within protein structure."},{"Start":"05:19.770 ","End":"05:22.040","Text":"We talked about protein conformations and"},{"Start":"05:22.040 ","End":"05:26.610","Text":"various stabilizing forces of protein conformation."}],"ID":29563},{"Watched":false,"Name":"Exercise 7","Duration":"34s","ChapterTopicVideoID":28330,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.350","Text":"In this exercise, we are going to test our knowledge on protein conformations."},{"Start":"00:04.350 ","End":"00:09.630","Text":"What forces stabilize the native conformation or conformations of a polypeptide chain?"},{"Start":"00:09.630 ","End":"00:13.980","Text":"Chemical interactions that stabilize the native conformation include disulfide bonds and"},{"Start":"00:13.980 ","End":"00:18.765","Text":"the weak non-covalent interactions we described in a previous chapter."},{"Start":"00:18.765 ","End":"00:20.820","Text":"These include, hydrogen bonds,"},{"Start":"00:20.820 ","End":"00:23.670","Text":"the hydrophobic effect, and ionic interactions."},{"Start":"00:23.670 ","End":"00:27.090","Text":"Now reminder, not all proteins have disulfide bonds."},{"Start":"00:27.090 ","End":"00:28.457","Text":"Many proteins do not,"},{"Start":"00:28.457 ","End":"00:31.695","Text":"but in those that there are disulfide bonds,"},{"Start":"00:31.695 ","End":"00:34.540","Text":"these are also stabilizing forces."}],"ID":29564},{"Watched":false,"Name":"Exercise 8","Duration":"2m 58s","ChapterTopicVideoID":28331,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.195","Text":"What did we learn in the lesson of protein conformation?"},{"Start":"00:03.195 ","End":"00:05.460","Text":"What is the solvation layer,"},{"Start":"00:05.460 ","End":"00:07.860","Text":"a hydration shell, and the hydration number?"},{"Start":"00:07.860 ","End":"00:12.510","Text":"The salvation layer is what forms when water surrounds a hydrophobic molecule."},{"Start":"00:12.510 ","End":"00:15.030","Text":"In general terms, salvation is the process of"},{"Start":"00:15.030 ","End":"00:18.630","Text":"association of molecules of a solvent with molecules of a solute."},{"Start":"00:18.630 ","End":"00:24.750","Text":"A synonym name for this is a solvation shell or solvation sheath."},{"Start":"00:24.750 ","End":"00:28.050","Text":"These are also terms for solvation layer."},{"Start":"00:28.050 ","End":"00:29.954","Text":"As ions dissolve in a solvent,"},{"Start":"00:29.954 ","End":"00:34.160","Text":"they spread out and become surrounded by solvent molecules."},{"Start":"00:34.160 ","End":"00:35.780","Text":"When the solvent is water,"},{"Start":"00:35.780 ","End":"00:41.240","Text":"it is referred to as a hydration shell or a hydration sphere."},{"Start":"00:41.240 ","End":"00:43.760","Text":"Since you have water molecules,"},{"Start":"00:43.760 ","End":"00:46.130","Text":"this is the oxygen with its partial negative charge,"},{"Start":"00:46.130 ","End":"00:49.190","Text":"and these are the hydrogens with their partial positive charge."},{"Start":"00:49.190 ","End":"00:51.650","Text":"Remember H_2O, this is the H,"},{"Start":"00:51.650 ","End":"00:54.155","Text":"the hydrogen, this is the oxygen."},{"Start":"00:54.155 ","End":"00:58.985","Text":"These water molecules surround the ions."},{"Start":"00:58.985 ","End":"01:03.875","Text":"They surround the molecules of the solute and create"},{"Start":"01:03.875 ","End":"01:12.340","Text":"the hydration sphere or hydration shell or solvation layer."},{"Start":"01:12.340 ","End":"01:16.776","Text":"Hydration is from the term water,"},{"Start":"01:16.776 ","End":"01:19.445","Text":"remember, like hydrophobic."},{"Start":"01:19.445 ","End":"01:24.275","Text":"This comes from the Greek for water and this is, in essence,"},{"Start":"01:24.275 ","End":"01:31.355","Text":"solvation layer that is formed when a solute is in water as its solvent."},{"Start":"01:31.355 ","End":"01:33.035","Text":"Now, going to the next term,"},{"Start":"01:33.035 ","End":"01:35.990","Text":"the number of solvent molecules surrounding each unit of"},{"Start":"01:35.990 ","End":"01:39.425","Text":"solute is called the hydration number of the solute."},{"Start":"01:39.425 ","End":"01:42.949","Text":"If you have this ion,"},{"Start":"01:42.949 ","End":"01:48.965","Text":"this molecule, it\u0027s surrounded by water molecules so in this case,"},{"Start":"01:48.965 ","End":"01:51.750","Text":"in this figure, hydrogens are gray and have"},{"Start":"01:51.750 ","End":"01:54.620","Text":"a partial positive charge and it is surrounding"},{"Start":"01:54.620 ","End":"02:00.950","Text":"this molecule and creating this hydration sphere or hydration shell or in general terms,"},{"Start":"02:00.950 ","End":"02:05.075","Text":"the solvation layer and there\u0027s a specific number of"},{"Start":"02:05.075 ","End":"02:10.235","Text":"solvent molecules surrounding the unit of solute and this is the hydration number,"},{"Start":"02:10.235 ","End":"02:12.780","Text":"if we count it, we see 6 here,"},{"Start":"02:12.780 ","End":"02:13.980","Text":"so the hydration number,"},{"Start":"02:13.980 ","End":"02:16.375","Text":"in this case, would be 6."},{"Start":"02:16.375 ","End":"02:19.850","Text":"Just to clarify, an example of this is when"},{"Start":"02:19.850 ","End":"02:24.394","Text":"water molecules are arranged around the metal ion as seen here and in this example,"},{"Start":"02:24.394 ","End":"02:25.835","Text":"we\u0027ll say a cation,"},{"Start":"02:25.835 ","End":"02:29.360","Text":"which means a positive charged ion,"},{"Start":"02:29.360 ","End":"02:33.590","Text":"the electronegative oxygen atom is attracted to the positive charge."},{"Start":"02:33.590 ","End":"02:41.660","Text":"You see the oxygen of the water molecules attracted to the positive charge of the cation,"},{"Start":"02:41.660 ","End":"02:46.295","Text":"and the result is a solvation shell of water molecules around it."},{"Start":"02:46.295 ","End":"02:49.055","Text":"This shell can be several molecules thick,"},{"Start":"02:49.055 ","End":"02:51.365","Text":"not necessarily just 1 layer."},{"Start":"02:51.365 ","End":"02:54.005","Text":"This is dependent upon the charge of the ion,"},{"Start":"02:54.005 ","End":"02:58.290","Text":"its distribution, and spatial dimensions."}],"ID":29565},{"Watched":false,"Name":"Exercise 9","Duration":"45s","ChapterTopicVideoID":28332,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.010","Text":"We are within protein conformations and we have another exercise."},{"Start":"00:05.010 ","End":"00:11.145","Text":"Explain this statement: Hydrogen bonds between groups in proteins form cooperatively."},{"Start":"00:11.145 ","End":"00:13.109","Text":"We think of cooperation,"},{"Start":"00:13.109 ","End":"00:14.520","Text":"helping each other out."},{"Start":"00:14.520 ","End":"00:16.860","Text":"The idea is that formation of"},{"Start":"00:16.860 ","End":"00:20.970","Text":"1 hydrogen bond facilitates the formation of additional hydrogen bonds."},{"Start":"00:20.970 ","End":"00:23.580","Text":"In this way, hydrogen bonds often have"},{"Start":"00:23.580 ","End":"00:26.655","Text":"an important role in guiding the protein folding process."},{"Start":"00:26.655 ","End":"00:29.310","Text":"Once 1 hydrogen bond forms,"},{"Start":"00:29.310 ","End":"00:34.370","Text":"there\u0027s a chain reaction that additional hydrogen bonds form and allow"},{"Start":"00:34.370 ","End":"00:39.560","Text":"for greater interaction and stabilize certain folding in structures,"},{"Start":"00:39.560 ","End":"00:44.849","Text":"and this can be a guiding force in protein folding."}],"ID":29566},{"Watched":false,"Name":"Exercise 10","Duration":"1m 15s","ChapterTopicVideoID":28333,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.360","Text":"We have another question within protein conformations."},{"Start":"00:03.360 ","End":"00:08.685","Text":"Most of the structural patterns we talked about reflect 2 simple rules. What are these?"},{"Start":"00:08.685 ","End":"00:14.040","Text":"What are the 2 simple rules that we mentioned with regard to structural patterns?"},{"Start":"00:14.040 ","End":"00:18.735","Text":"The 2 rules that are reflected by most of the structural patterns of proteins are; 1,"},{"Start":"00:18.735 ","End":"00:24.720","Text":"hydrophobic residues are largely buried in the protein interior away from water,"},{"Start":"00:24.720 ","End":"00:31.245","Text":"and 2, the number of hydrogen bonds within the protein is maximized."},{"Start":"00:31.245 ","End":"00:33.420","Text":"Insoluble proteins and proteins within"},{"Start":"00:33.420 ","End":"00:37.200","Text":"membranes follow somewhat different rules because of their function on their environment,"},{"Start":"00:37.200 ","End":"00:40.610","Text":"but weak interactions are still critical structural elements."},{"Start":"00:40.610 ","End":"00:44.160","Text":"Anyhow, we didn\u0027t expand on this more in this lesson,"},{"Start":"00:44.160 ","End":"00:51.770","Text":"but the idea is that the number of hydrogen bonds within the protein tends to maximize."},{"Start":"00:51.770 ","End":"00:57.185","Text":"We talked about the cooperative effect where once 1 hydrogen bond forms,"},{"Start":"00:57.185 ","End":"01:01.160","Text":"additional form as a chain reaction so"},{"Start":"01:01.160 ","End":"01:05.555","Text":"that you have as many hydrogen bonds that can possibly interact."},{"Start":"01:05.555 ","End":"01:09.170","Text":"The number is maximized and this tends to"},{"Start":"01:09.170 ","End":"01:14.760","Text":"stabilize structure and therefore is important in protein conformations."}],"ID":29567},{"Watched":false,"Name":"Peptide Bonds","Duration":"9m 42s","ChapterTopicVideoID":28334,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.230 ","End":"00:06.405","Text":"We\u0027re going to be talking about peptide bonds as part of the topic of protein structure."},{"Start":"00:06.405 ","End":"00:08.850","Text":"By the end of this section, you\u0027ll be able to define"},{"Start":"00:08.850 ","End":"00:13.350","Text":"the peptide bond and associate peptide bonds and conformations."},{"Start":"00:13.350 ","End":"00:18.525","Text":"The peptide bond is rigid and planar and is part of the primary structure."},{"Start":"00:18.525 ","End":"00:23.460","Text":"Covalent bonds also play a role in the conformation of a polypeptide."},{"Start":"00:23.460 ","End":"00:28.080","Text":"Extra diffraction studies of crystals of amino acids and of simple dipeptides"},{"Start":"00:28.080 ","End":"00:32.780","Text":"and tripeptides demonstrated that the peptide carbon-nitrogen,"},{"Start":"00:32.780 ","End":"00:36.080","Text":"the C-N bond, and these is somewhat"},{"Start":"00:36.080 ","End":"00:40.770","Text":"shorter than that C-N carbon-nitrogen bond in a simple amine,"},{"Start":"00:40.770 ","End":"00:44.690","Text":"and that the atoms associated with the peptide bond are co-planar."},{"Start":"00:44.690 ","End":"00:45.860","Text":"If you look here,"},{"Start":"00:45.860 ","End":"00:47.195","Text":"you have the peptide bond,"},{"Start":"00:47.195 ","End":"00:48.860","Text":"and this is a dipeptide."},{"Start":"00:48.860 ","End":"00:51.740","Text":"You have the carbon-nitrogen bond,"},{"Start":"00:51.740 ","End":"00:57.095","Text":"and this is shorter than the carbon-nitrogen bond found in an amine."},{"Start":"00:57.095 ","End":"01:01.610","Text":"This indicated partial sharing of 2 pairs of electrons between"},{"Start":"01:01.610 ","End":"01:06.335","Text":"the carbonyl oxygen and the amide nitrogen."},{"Start":"01:06.335 ","End":"01:11.195","Text":"The oxygen has a partial negative charge and the nitrogen a partial positive charge,"},{"Start":"01:11.195 ","End":"01:14.330","Text":"setting up a small electric dipole."},{"Start":"01:14.330 ","End":"01:17.984","Text":"What you see here, you have 2 amino acids."},{"Start":"01:17.984 ","End":"01:23.775","Text":"They\u0027ll come together and this will form this peptide bond."},{"Start":"01:23.775 ","End":"01:28.985","Text":"The 6 atoms of the peptide group on a single plane with"},{"Start":"01:28.985 ","End":"01:34.955","Text":"the oxygen atom of the carbonyl group and the hydrogen atom of amide nitrogen,"},{"Start":"01:34.955 ","End":"01:37.370","Text":"and they are trans to each other."},{"Start":"01:37.370 ","End":"01:40.385","Text":"These are on the opposite sides of this double bond."},{"Start":"01:40.385 ","End":"01:42.050","Text":"They are considered trans."},{"Start":"01:42.050 ","End":"01:43.970","Text":"They\u0027re opposite of this double bond which is"},{"Start":"01:43.970 ","End":"01:47.540","Text":"actually the peptide bonds that link amino acid residues and"},{"Start":"01:47.540 ","End":"01:50.720","Text":"a polypeptide that are formed in a condensation reaction"},{"Start":"01:50.720 ","End":"01:52.880","Text":"between the acidic carboxyl group of"},{"Start":"01:52.880 ","End":"01:55.865","Text":"1 amino acid and the basic amino group of another amino acid."},{"Start":"01:55.865 ","End":"01:58.490","Text":"The context of a peptide,"},{"Start":"01:58.490 ","End":"02:05.525","Text":"the amide group CO-NH is referred to as the peptide group."},{"Start":"02:05.525 ","End":"02:08.960","Text":"This is considered the peptide group."},{"Start":"02:08.960 ","End":"02:15.800","Text":"Here you see these form a bond by having a condensation reaction."},{"Start":"02:15.800 ","End":"02:17.480","Text":"This is squeezed out,"},{"Start":"02:17.480 ","End":"02:20.525","Text":"this H2O, therefore a condensation reaction."},{"Start":"02:20.525 ","End":"02:23.720","Text":"It condenses, water is squeezed out,"},{"Start":"02:23.720 ","End":"02:27.965","Text":"and then what you have is the oxygen,"},{"Start":"02:27.965 ","End":"02:29.420","Text":"the CO right here,"},{"Start":"02:29.420 ","End":"02:34.870","Text":"this carbon-oxygen attaching to the NH here."},{"Start":"02:34.870 ","End":"02:36.780","Text":"These will form this bond,"},{"Start":"02:36.780 ","End":"02:44.470","Text":"the CO-NH and this is referred to as the peptide group."},{"Start":"02:44.470 ","End":"02:47.660","Text":"These are on a single plane."},{"Start":"02:47.660 ","End":"02:50.060","Text":"Linus Pauling and Robert Corey,"},{"Start":"02:50.060 ","End":"02:52.970","Text":"who\u0027s studied the peptide bond in the late 1930s"},{"Start":"02:52.970 ","End":"02:56.389","Text":"concluded that and came up with these findings"},{"Start":"02:56.389 ","End":"02:59.810","Text":"that the peptide carbon-nitrogen bonds are unable to"},{"Start":"02:59.810 ","End":"03:03.880","Text":"rotate freely because of their partial double bond character."},{"Start":"03:03.880 ","End":"03:05.570","Text":"As you could see here again,"},{"Start":"03:05.570 ","End":"03:07.010","Text":"this double bond character,"},{"Start":"03:07.010 ","End":"03:13.265","Text":"it restricts the ability of these carbon nitrogen bonds to move freely."},{"Start":"03:13.265 ","End":"03:18.920","Text":"These can\u0027t just move freely because of these double bonds."},{"Start":"03:18.920 ","End":"03:26.720","Text":"Rotation was shown to be permitted about the N carbon Alpha and the carbon Alpha C bonds."},{"Start":"03:26.720 ","End":"03:29.195","Text":"If you\u0027re looking here, we have the carbon Alphas."},{"Start":"03:29.195 ","End":"03:31.090","Text":"If you look here,"},{"Start":"03:31.090 ","End":"03:34.760","Text":"you have N carbon Alpha and carbon Alpha carbon,"},{"Start":"03:34.760 ","End":"03:39.065","Text":"there is rotation that is permitted in these 2,"},{"Start":"03:39.065 ","End":"03:45.440","Text":"see here, N carbon Alpha and carbon Alpha carbon rotation is permitted here,"},{"Start":"03:45.440 ","End":"03:49.850","Text":"and this is what these arrows indicate that there can be some movement,"},{"Start":"03:49.850 ","End":"03:54.110","Text":"whereas when you\u0027re looking between the N-C,"},{"Start":"03:54.110 ","End":"03:57.485","Text":"it is rigid and rotation is not permitted."},{"Start":"03:57.485 ","End":"03:58.925","Text":"What we see here?"},{"Start":"03:58.925 ","End":"04:02.270","Text":"The carbonyl oxygen has a partial negative charge and that amide nitrogen,"},{"Start":"04:02.270 ","End":"04:05.585","Text":"a partial positive charge setting up a small electric dipole."},{"Start":"04:05.585 ","End":"04:11.525","Text":"Virtually all peptide bonds in proteins occur in this trans configuration."},{"Start":"04:11.525 ","End":"04:15.320","Text":"There is the negative and the positive charge and there\u0027s that interaction."},{"Start":"04:15.320 ","End":"04:18.500","Text":"The carboxyl oxygen has a partial negative charge while"},{"Start":"04:18.500 ","End":"04:22.310","Text":"the amide nitrogen has a partial positive charge,"},{"Start":"04:22.310 ","End":"04:25.460","Text":"setting up a small electric dipole here."},{"Start":"04:25.460 ","End":"04:28.730","Text":"Virtually all peptide bonds in proteins occur in"},{"Start":"04:28.730 ","End":"04:34.130","Text":"this trans configuration where the oxygen is on this side of the double bond,"},{"Start":"04:34.130 ","End":"04:38.450","Text":"while the hydrogen is on the other side of the double bond,"},{"Start":"04:38.450 ","End":"04:41.780","Text":"and then therefore is considered trans."},{"Start":"04:41.780 ","End":"04:43.504","Text":"Now if we look further,"},{"Start":"04:43.504 ","End":"04:45.050","Text":"each peptide bond has"},{"Start":"04:45.050 ","End":"04:48.920","Text":"some double bond character due to the resonance and it cannot rotate,"},{"Start":"04:48.920 ","End":"04:53.850","Text":"so 3 bonds separate sequential Alpha carbons in a polypeptide chain."},{"Start":"04:53.850 ","End":"04:56.405","Text":"You have the N-C Alpha,"},{"Start":"04:56.405 ","End":"05:00.695","Text":"as you see here, you have the C Alpha C,"},{"Start":"05:00.695 ","End":"05:02.285","Text":"as you see here."},{"Start":"05:02.285 ","End":"05:07.805","Text":"The C Alpha C right here and C Alpha C, which can rotate."},{"Start":"05:07.805 ","End":"05:11.210","Text":"These have the bond angles of Phi and Psi."},{"Start":"05:11.210 ","End":"05:15.260","Text":"The peptide carbon-nitrogen bond is not free to rotate."},{"Start":"05:15.260 ","End":"05:17.960","Text":"Other single bonds in the backbone may also be rotationally"},{"Start":"05:17.960 ","End":"05:21.050","Text":"hindered depending on the size and charge of the R groups."},{"Start":"05:21.050 ","End":"05:25.300","Text":"The R groups are represented here by this purple ball."},{"Start":"05:25.300 ","End":"05:28.550","Text":"Their size can, if it\u0027s really big,"},{"Start":"05:28.550 ","End":"05:30.720","Text":"hinder any additional movement."},{"Start":"05:30.720 ","End":"05:34.600","Text":"As one looks out from the Alpha carbon,"},{"Start":"05:34.600 ","End":"05:42.065","Text":"Psi and the Phi angles increase as the carbonyl or amide nitrogens rotate clockwise."},{"Start":"05:42.065 ","End":"05:45.630","Text":"Rotation is permitted about the N-C Alpha and"},{"Start":"05:45.630 ","End":"05:51.545","Text":"the C Alpha C bonds as shown here and designated by these arrows."},{"Start":"05:51.545 ","End":"05:56.330","Text":"The backbone of a polypeptide chain can thus be visualized as a series of"},{"Start":"05:56.330 ","End":"06:02.120","Text":"rigid planes with consecutive planes sharing a common point of rotation at C Alpha."},{"Start":"06:02.120 ","End":"06:04.205","Text":"Meaning if you see here,"},{"Start":"06:04.205 ","End":"06:05.725","Text":"this is plane 1,"},{"Start":"06:05.725 ","End":"06:07.360","Text":"this is plane 2."},{"Start":"06:07.360 ","End":"06:09.320","Text":"Just for this example,"},{"Start":"06:09.320 ","End":"06:11.465","Text":"this could be considered plane 3 and plane 4."},{"Start":"06:11.465 ","End":"06:13.790","Text":"If you\u0027re looking at these 2 planes, well,"},{"Start":"06:13.790 ","End":"06:18.140","Text":"you\u0027re seeing a common point of rotation is C Alpha,"},{"Start":"06:18.140 ","End":"06:23.855","Text":"meaning that the 2 planes that are next to each other share this central point."},{"Start":"06:23.855 ","End":"06:29.265","Text":"This is the C Alpha and it\u0027s a central point between them which permits rotation,"},{"Start":"06:29.265 ","End":"06:31.800","Text":"same as between these 2 planes,"},{"Start":"06:31.800 ","End":"06:34.735","Text":"plane 2 and plane 3."},{"Start":"06:34.735 ","End":"06:37.595","Text":"The C Alpha, this gray one,"},{"Start":"06:37.595 ","End":"06:44.015","Text":"is what permits rotation amongst this common point between plane 2 and plane 3."},{"Start":"06:44.015 ","End":"06:46.940","Text":"Same goes if we look at plane 4,"},{"Start":"06:46.940 ","End":"06:52.595","Text":"C Alpha, this is the common point between them that allows rotation."},{"Start":"06:52.595 ","End":"06:55.490","Text":"The rigid peptide bonds limit the range of"},{"Start":"06:55.490 ","End":"07:00.050","Text":"confirmations that can be presumed of a polypeptide chain."},{"Start":"07:00.050 ","End":"07:06.065","Text":"Peptide confirmation is actually defined by 3 dihedral angles,"},{"Start":"07:06.065 ","End":"07:08.360","Text":"also known as torsion angles,"},{"Start":"07:08.360 ","End":"07:12.395","Text":"and these are called Phi, as mentioned before,"},{"Start":"07:12.395 ","End":"07:16.610","Text":"between the nitrogen and the Alpha carbon and"},{"Start":"07:16.610 ","End":"07:22.220","Text":"Psi between the Alpha carbon and the carbon and the third torsion angle,"},{"Start":"07:22.220 ","End":"07:25.385","Text":"the third dihedral angle is Omega,"},{"Start":"07:25.385 ","End":"07:27.770","Text":"which we haven\u0027t mentioned yet."},{"Start":"07:27.770 ","End":"07:33.230","Text":"Reflecting rotation about each of the 3 repeating bonds in the peptide backbone,"},{"Start":"07:33.230 ","End":"07:37.490","Text":"a dihedral angle is the angle at the intersection of 2 planes."},{"Start":"07:37.490 ","End":"07:38.660","Text":"In the case of peptides,"},{"Start":"07:38.660 ","End":"07:42.395","Text":"the planes are defined by bond vectors in the peptide backbone,"},{"Start":"07:42.395 ","End":"07:47.120","Text":"meaning the bonds between these angles,"},{"Start":"07:47.120 ","End":"07:51.870","Text":"between the 2 planes of these bonds are the dihedral angles,"},{"Start":"07:51.870 ","End":"07:56.025","Text":"so 2 successive bond vectors describe a plane."},{"Start":"07:56.025 ","End":"07:59.180","Text":"These 2 basically describe a plane."},{"Start":"07:59.180 ","End":"08:02.720","Text":"3 successive bond vectors describe 2 planes."},{"Start":"08:02.720 ","End":"08:05.300","Text":"If we\u0027re looking at here, here,"},{"Start":"08:05.300 ","End":"08:10.235","Text":"and here, this already is going through 2 planes."},{"Start":"08:10.235 ","End":"08:11.720","Text":"The central bond,"},{"Start":"08:11.720 ","End":"08:13.790","Text":"so if you have all these,"},{"Start":"08:13.790 ","End":"08:15.725","Text":"or if we\u0027re looking here,"},{"Start":"08:15.725 ","End":"08:17.690","Text":"if we\u0027re looking at these 3,"},{"Start":"08:17.690 ","End":"08:21.425","Text":"the central bond vector is common to both planes."},{"Start":"08:21.425 ","End":"08:27.200","Text":"The angle between these 2 planes is what is measured to describe peptide conformation."},{"Start":"08:27.200 ","End":"08:29.105","Text":"When you\u0027re looking here,"},{"Start":"08:29.105 ","End":"08:35.435","Text":"the angles between the bonds are measured and describe the peptide conformation."},{"Start":"08:35.435 ","End":"08:38.700","Text":"The Omega angle is the one we didn\u0027t really explain."},{"Start":"08:38.700 ","End":"08:42.290","Text":"Is the angle on a peptide that is measured over the peptide bond,"},{"Start":"08:42.290 ","End":"08:43.760","Text":"the chemical bond that connects"},{"Start":"08:43.760 ","End":"08:49.044","Text":"the 2 amino acids and has a little bit of a double-bonded character."},{"Start":"08:49.044 ","End":"08:53.435","Text":"Because of this, if we look in and are reminded here,"},{"Start":"08:53.435 ","End":"08:56.975","Text":"this is the Omega bond right here,"},{"Start":"08:56.975 ","End":"08:59.675","Text":"it is almost a 180 degrees."},{"Start":"08:59.675 ","End":"09:05.420","Text":"In other words, it describes the third possible torsion angle within the protein."},{"Start":"09:05.420 ","End":"09:07.540","Text":"Again, looking here you\u0027ve got 1,"},{"Start":"09:07.540 ","End":"09:09.762","Text":"2, and then here,"},{"Start":"09:09.762 ","End":"09:12.320","Text":"this is the bond, the Omega bond."},{"Start":"09:12.320 ","End":"09:18.050","Text":"It describes the third possible torsion angle within the protein backbone called Omega."},{"Start":"09:18.050 ","End":"09:21.230","Text":"It describes the rotation at the peptide bond which is"},{"Start":"09:21.230 ","End":"09:25.190","Text":"mostly flat and fixed to 180 degrees."},{"Start":"09:25.190 ","End":"09:30.935","Text":"You basically see that it forms a 180 degrees with other bonds around it."},{"Start":"09:30.935 ","End":"09:35.690","Text":"With this, we concluded the section covering peptide bonds within protein structure,"},{"Start":"09:35.690 ","End":"09:38.165","Text":"and we learned how to define the peptide bond"},{"Start":"09:38.165 ","End":"09:42.360","Text":"and associate peptide bonds and conformations."}],"ID":29568},{"Watched":false,"Name":"Exercise 11","Duration":"55s","ChapterTopicVideoID":28335,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.810","Text":"We\u0027re diving into an exercise on peptide bonds."},{"Start":"00:03.810 ","End":"00:06.720","Text":"What can be said about the peptide C-N bond,"},{"Start":"00:06.720 ","End":"00:08.610","Text":"the carbon nitrogen bond?"},{"Start":"00:08.610 ","End":"00:13.515","Text":"First off, the peptide bond is rigid and planar and is part of the primary structure."},{"Start":"00:13.515 ","End":"00:16.850","Text":"Rigid means stable, it\u0027s strong, planar,"},{"Start":"00:16.850 ","End":"00:21.200","Text":"it has a 3D orientation, planes and space."},{"Start":"00:21.200 ","End":"00:24.080","Text":"It plays a role in the conformation of a polypeptide,"},{"Start":"00:24.080 ","End":"00:28.030","Text":"and it is shorter than the C-N bond in a simple amine."},{"Start":"00:28.030 ","End":"00:31.760","Text":"The atoms associated with the peptide bond are co-planar."},{"Start":"00:31.760 ","End":"00:34.325","Text":"They sit on 2 planes."},{"Start":"00:34.325 ","End":"00:37.430","Text":"Furthermore, the peptide carbon nitrogen bonds, the C-N bonds,"},{"Start":"00:37.430 ","End":"00:40.970","Text":"are unable to rotate freely because of their partial double bond character."},{"Start":"00:40.970 ","End":"00:44.465","Text":"Remember, it seems like they have 2 hands that are bonding them."},{"Start":"00:44.465 ","End":"00:49.250","Text":"Now you could add any additional information that you remember from the lesson that"},{"Start":"00:49.250 ","End":"00:54.810","Text":"is relevant and relates to the peptide carbon nitrogen bond."}],"ID":29569},{"Watched":false,"Name":"Exercise 12","Duration":"4m 14s","ChapterTopicVideoID":28336,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.240","Text":"We\u0027re here with another exercise covering peptide bonds."},{"Start":"00:03.240 ","End":"00:05.955","Text":"Complete the sentence, fill in the blanks."},{"Start":"00:05.955 ","End":"00:12.000","Text":"Part 1: The___ atoms of the____ group are in a ____ plane,"},{"Start":"00:12.000 ","End":"00:14.280","Text":"with the oxygen atom of the carbonyl group and"},{"Start":"00:14.280 ","End":"00:17.625","Text":"the hydrogen atom of the amide nitrogen ____ to each other."},{"Start":"00:17.625 ","End":"00:21.330","Text":"Let us start with thinking about the blank atoms of"},{"Start":"00:21.330 ","End":"00:27.585","Text":"the specific group that we covered throughout the lesson are in a specific plane."},{"Start":"00:27.585 ","End":"00:29.580","Text":"What group did we talk about,"},{"Start":"00:29.580 ","End":"00:31.920","Text":"and what about these atoms?"},{"Start":"00:31.920 ","End":"00:34.500","Text":"These are either specific atoms or maybe a number."},{"Start":"00:34.500 ","End":"00:36.690","Text":"Did we talk about a number of atoms in"},{"Start":"00:36.690 ","End":"00:39.710","Text":"a specific group that are in a certain plane? Well, yeah."},{"Start":"00:39.710 ","End":"00:43.850","Text":"We actually mentioned that the 6 atoms of,"},{"Start":"00:43.850 ","End":"00:46.160","Text":"and what is the group that we\u0027re talking about?"},{"Start":"00:46.160 ","End":"00:49.595","Text":"This section is what peptide bonds."},{"Start":"00:49.595 ","End":"00:52.070","Text":"The group that we\u0027re talking about is the 6 atoms of"},{"Start":"00:52.070 ","End":"00:57.125","Text":"the peptide group are in a what plane?"},{"Start":"00:57.125 ","End":"01:01.640","Text":"We mentioned that it\u0027s rigid and in a single plane."},{"Start":"01:01.640 ","End":"01:04.910","Text":"The 6 atoms of the peptide group are in single plane,"},{"Start":"01:04.910 ","End":"01:10.735","Text":"with the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen,"},{"Start":"01:10.735 ","End":"01:12.390","Text":"what to each other?"},{"Start":"01:12.390 ","End":"01:13.740","Text":"Trans to each other."},{"Start":"01:13.740 ","End":"01:17.265","Text":"Remember trans means on opposite directions."},{"Start":"01:17.265 ","End":"01:22.415","Text":"If you have what we think of as a double bond,"},{"Start":"01:22.415 ","End":"01:25.540","Text":"trans means that it will be here,"},{"Start":"01:25.540 ","End":"01:32.525","Text":"and if we talk about oxygen atom and the hydrogen atom, this is trans."},{"Start":"01:32.525 ","End":"01:34.385","Text":"We add cis and trans."},{"Start":"01:34.385 ","End":"01:36.470","Text":"We covered this in a previous section."},{"Start":"01:36.470 ","End":"01:41.525","Text":"Cis would mean that the oxygen and the hydrogen are on the same side of"},{"Start":"01:41.525 ","End":"01:47.870","Text":"this bond whereas trans means they are on opposite sides."},{"Start":"01:47.870 ","End":"01:51.215","Text":"Let\u0027s move to Part 2. The peptide ____that link"},{"Start":"01:51.215 ","End":"01:55.568","Text":"amino acid residues in a polypeptide are formed in a"},{"Start":"01:55.568 ","End":"01:59.300","Text":"____ reaction between the acidic carboxyl group of"},{"Start":"01:59.300 ","End":"02:03.245","Text":"1 amino acid and the basic amino group of another amino acid."},{"Start":"02:03.245 ","End":"02:04.850","Text":"In the context of a peptide,"},{"Start":"02:04.850 ","End":"02:10.285","Text":"the amide group (CO-NH) is referred to as the ____ ____."},{"Start":"02:10.285 ","End":"02:12.560","Text":"Let\u0027s focus on the first sentence."},{"Start":"02:12.560 ","End":"02:16.490","Text":"The peptide something that link amino acid residues in"},{"Start":"02:16.490 ","End":"02:22.305","Text":"a polypeptide are formed in a what reaction? What did we talk about?"},{"Start":"02:22.305 ","End":"02:26.390","Text":"The peptide bond, this whole section we\u0027re talking about peptide bonds."},{"Start":"02:26.390 ","End":"02:30.020","Text":"The peptide bonds that link amino acid residues in a polypeptide,"},{"Start":"02:30.020 ","End":"02:36.590","Text":"and you had a clue that link here versus links means plural."},{"Start":"02:36.590 ","End":"02:38.960","Text":"The peptide bonds that link amino acid residues in"},{"Start":"02:38.960 ","End":"02:43.100","Text":"a polypeptide are formed in a what kind of reaction?"},{"Start":"02:43.100 ","End":"02:49.580","Text":"A condensation reaction, meaning that a water molecule has been eliminated,"},{"Start":"02:49.580 ","End":"02:51.140","Text":"has been squeezed out."},{"Start":"02:51.140 ","End":"02:53.540","Text":"The peptide bonds that link amino acid residues in"},{"Start":"02:53.540 ","End":"02:56.300","Text":"a polypeptide are formed in a condensation reaction between"},{"Start":"02:56.300 ","End":"02:58.685","Text":"the acidic carboxyl group of 1 amino acid"},{"Start":"02:58.685 ","End":"03:01.340","Text":"and the basic amino group of another amino acid."},{"Start":"03:01.340 ","End":"03:05.090","Text":"Now, the clue to it being a condensation is the fact that it\u0027s acid and base."},{"Start":"03:05.090 ","End":"03:12.110","Text":"You have a proton donor or a proton acceptor or a hydroxide donor."},{"Start":"03:12.110 ","End":"03:14.270","Text":"Meaning if you have acid,"},{"Start":"03:14.270 ","End":"03:15.590","Text":"it\u0027s giving the H+."},{"Start":"03:15.590 ","End":"03:16.670","Text":"If you have a base,"},{"Start":"03:16.670 ","End":"03:20.945","Text":"it\u0027s giving the OH- it comes together condensation reaction,"},{"Start":"03:20.945 ","End":"03:23.390","Text":"and you have H2O."},{"Start":"03:23.390 ","End":"03:26.465","Text":"This touches up on previous lessons."},{"Start":"03:26.465 ","End":"03:30.935","Text":"Now, next sentence in the context of a peptide, the amide group,"},{"Start":"03:30.935 ","End":"03:37.030","Text":"carbon-oxygen bonded to nitrogen-hydrogen is referred to as the?"},{"Start":"03:37.030 ","End":"03:39.030","Text":"What were we talking about here?"},{"Start":"03:39.030 ","End":"03:41.355","Text":"In the context of a peptide,"},{"Start":"03:41.355 ","End":"03:47.655","Text":"the amide group is referred to as the peptide group."},{"Start":"03:47.655 ","End":"03:50.760","Text":"This is referred to the peptide group."},{"Start":"03:50.760 ","End":"03:53.690","Text":"Part 2, the answer is the peptide bonds that link"},{"Start":"03:53.690 ","End":"03:56.180","Text":"amino acid residues in a polypeptide are formed in"},{"Start":"03:56.180 ","End":"03:59.180","Text":"a condensation reaction between the acidic carboxyl group of"},{"Start":"03:59.180 ","End":"04:03.425","Text":"1 amino acid and the basic amino group of another amino acid."},{"Start":"04:03.425 ","End":"04:05.270","Text":"In the context of a peptide,"},{"Start":"04:05.270 ","End":"04:07.505","Text":"the amide group carbon-oxygen bond to"},{"Start":"04:07.505 ","End":"04:12.930","Text":"nitrogen-hydrogen (CO-NH) is referred to as the peptide group."}],"ID":29570},{"Watched":false,"Name":"Exercise 13","Duration":"1m 47s","ChapterTopicVideoID":28337,"CourseChapterTopicPlaylistID":281855,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.379","Text":"We\u0027re diving into another exercise within peptide bonds."},{"Start":"00:04.379 ","End":"00:07.110","Text":"What did Linus Pauling and Robert Corey conclude with"},{"Start":"00:07.110 ","End":"00:10.440","Text":"regard to the peptide bond in the late 1930s?"},{"Start":"00:10.440 ","End":"00:12.690","Text":"Linus Pauling and Robert Corey,"},{"Start":"00:12.690 ","End":"00:15.390","Text":"who studied the peptide bond in the late 1930s,"},{"Start":"00:15.390 ","End":"00:18.150","Text":"concluded that the peptide carbon-nitrogen bonds,"},{"Start":"00:18.150 ","End":"00:19.290","Text":"the C-N bonds,"},{"Start":"00:19.290 ","End":"00:23.520","Text":"are unable to rotate freely because of their partial double bond character."},{"Start":"00:23.520 ","End":"00:27.870","Text":"Rotation is permitted about the N-C Alpha,"},{"Start":"00:27.870 ","End":"00:32.975","Text":"nitrogen-carbon Alpha, and the carbon Alpha and carbon bonds."},{"Start":"00:32.975 ","End":"00:37.310","Text":"The backbone of a polypeptide chain can thus be visualized as a series of"},{"Start":"00:37.310 ","End":"00:43.690","Text":"rigid planes with consecutive planes sharing a common point of rotation at C Alpha."},{"Start":"00:43.690 ","End":"00:46.730","Text":"If you see here the C Alpha,"},{"Start":"00:46.730 ","End":"00:50.705","Text":"meaning that the 2 planes that are next to each other,"},{"Start":"00:50.705 ","End":"00:52.865","Text":"this plane and this plane,"},{"Start":"00:52.865 ","End":"00:55.505","Text":"share a central point."},{"Start":"00:55.505 ","End":"00:57.035","Text":"This is the central point."},{"Start":"00:57.035 ","End":"00:58.490","Text":"If this is plane 1,"},{"Start":"00:58.490 ","End":"01:00.680","Text":"and this is plane 2,"},{"Start":"01:00.680 ","End":"01:03.079","Text":"and I\u0027m looking at these blue rectangles,"},{"Start":"01:03.079 ","End":"01:05.060","Text":"they represent a plane in space,"},{"Start":"01:05.060 ","End":"01:08.905","Text":"if these 2 planes, the common point."},{"Start":"01:08.905 ","End":"01:15.740","Text":"C Alpha is the common point between them at which it actually permits rotation."},{"Start":"01:15.740 ","End":"01:19.700","Text":"Rotation, as you could see what these arrows, is permitted here,"},{"Start":"01:19.700 ","End":"01:22.395","Text":"there\u0027s some movement that can happen there,"},{"Start":"01:22.395 ","End":"01:25.565","Text":"while as for other areas,"},{"Start":"01:25.565 ","End":"01:28.005","Text":"rotation is actually limited."},{"Start":"01:28.005 ","End":"01:30.590","Text":"The rigid peptide bonds limit the range of"},{"Start":"01:30.590 ","End":"01:34.820","Text":"confirmations that can be presumed of a polypeptide chain."},{"Start":"01:34.820 ","End":"01:40.160","Text":"This was the conclusion and what was brought forth by"},{"Start":"01:40.160 ","End":"01:46.290","Text":"Linus Pauling and Robert Corey who studied the peptide bonds in the late 1930s."}],"ID":29571}],"Thumbnail":null,"ID":281855},{"Name":"Higher Order Structure","TopicPlaylistFirstVideoID":0,"Duration":null,"Videos":[{"Watched":false,"Name":"Secondary Structure Part 1","Duration":"13m 23s","ChapterTopicVideoID":28347,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.475","Text":"As we continue to talk about protein structure,"},{"Start":"00:02.475 ","End":"00:06.210","Text":"we are going to expand and elaborate about protein\u0027s secondary structure."},{"Start":"00:06.210 ","End":"00:08.790","Text":"By the end of this section, you\u0027ll be able to define"},{"Start":"00:08.790 ","End":"00:13.620","Text":"protein spatial arrangement and alpha-helix conformation and orientation."},{"Start":"00:13.620 ","End":"00:16.185","Text":"We\u0027re splitting this lecture into 3 parts."},{"Start":"00:16.185 ","End":"00:17.655","Text":"Let\u0027s start with the first part."},{"Start":"00:17.655 ","End":"00:20.010","Text":"The term secondary structure refers to"},{"Start":"00:20.010 ","End":"00:26.174","Text":"any chosen segment of some polypeptide chain and describes"},{"Start":"00:26.174 ","End":"00:28.830","Text":"the local spatial arrangement of"},{"Start":"00:28.830 ","End":"00:31.590","Text":"its main chain atoms without"},{"Start":"00:31.590 ","End":"00:36.220","Text":"regard to its side chains or its relationship to other segments."},{"Start":"00:36.590 ","End":"00:40.880","Text":"The discussion of secondary structure mostly focuses on"},{"Start":"00:40.880 ","End":"00:45.810","Text":"common regular folding patterns of the polypeptide backbone."},{"Start":"00:46.240 ","End":"00:54.265","Text":"A few types of secondary structure are particularly stable and occur widely in proteins."},{"Start":"00:54.265 ","End":"00:59.570","Text":"The most prominent are the alpha helix and beta conformations,"},{"Start":"00:59.570 ","End":"01:01.070","Text":"which we\u0027ll describe shortly."},{"Start":"01:01.070 ","End":"01:04.499","Text":"Another common type is the beta-turn."},{"Start":"01:04.750 ","End":"01:08.150","Text":"Using fundamental chemical principles and"},{"Start":"01:08.150 ","End":"01:12.110","Text":"a few experimental observations, Pauling and Corey,"},{"Start":"01:12.110 ","End":"01:14.660","Text":"the scientists that study peptides that we mentioned in"},{"Start":"01:14.660 ","End":"01:18.925","Text":"an earlier section predicted the existence of these secondary structures."},{"Start":"01:18.925 ","End":"01:25.415","Text":"In 1951, several years before the first complete protein structure was elucidated,"},{"Start":"01:25.415 ","End":"01:31.080","Text":"common secondary structures have characteristic bond angles and amino acid content."},{"Start":"01:31.080 ","End":"01:32.465","Text":"If you look here,"},{"Start":"01:32.465 ","End":"01:36.215","Text":"there\u0027s this helical confirmation."},{"Start":"01:36.215 ","End":"01:42.979","Text":"Here you see 3 helices arranging together and then they arranged to create this fiber."},{"Start":"01:42.979 ","End":"01:44.630","Text":"You see here a tube,"},{"Start":"01:44.630 ","End":"01:51.845","Text":"that is also formed by this regular arrangement and you see here,"},{"Start":"01:51.845 ","End":"01:53.375","Text":"and you see an actin,"},{"Start":"01:53.375 ","End":"01:57.780","Text":"also 2 helices that are forming together."},{"Start":"01:57.780 ","End":"02:00.395","Text":"In the bond chain figure,"},{"Start":"02:00.395 ","End":"02:06.590","Text":"you see this is the same thing so you\u0027re seeing how these look."},{"Start":"02:06.590 ","End":"02:09.005","Text":"This is the amino acid portion."},{"Start":"02:09.005 ","End":"02:12.275","Text":"This is the 3 helices performing together, etc."},{"Start":"02:12.275 ","End":"02:17.990","Text":"The alpha-helix and beta conformation are the major repetitive secondary structures,"},{"Start":"02:17.990 ","End":"02:23.045","Text":"other repetitive structures do exist in some specialized proteins."},{"Start":"02:23.045 ","End":"02:25.445","Text":"An example of this is collagen."},{"Start":"02:25.445 ","End":"02:30.740","Text":"This is an important protein even more it\u0027s the most abundant protein in the human body."},{"Start":"02:30.740 ","End":"02:33.185","Text":"It is found in bones,"},{"Start":"02:33.185 ","End":"02:36.710","Text":"it\u0027s found in muscles, skin,"},{"Start":"02:36.710 ","End":"02:44.525","Text":"and tendons of 3 helices that come together that are made of a repeating tripeptide."},{"Start":"02:44.525 ","End":"02:49.145","Text":"You see here, this is the tripeptide and this is gly,"},{"Start":"02:49.145 ","End":"02:50.645","Text":"x, and pro."},{"Start":"02:50.645 ","End":"02:53.240","Text":"Going back to earlier lessons,"},{"Start":"02:53.240 ","End":"02:55.100","Text":"gly, let\u0027s think,"},{"Start":"02:55.100 ","End":"02:57.125","Text":"do you remember what it stands for?"},{"Start":"02:57.125 ","End":"02:59.675","Text":"I\u0027m going to let you think about it and try to remember."},{"Start":"02:59.675 ","End":"03:06.380","Text":"The x actually can be any of various other amino acid residues."},{"Start":"03:06.380 ","End":"03:15.710","Text":"So this can be a variety of amino acids and sometimes pro is actually replaced by hyp."},{"Start":"03:15.710 ","End":"03:21.470","Text":"Now, this should not necessarily be familiar to you, so let\u0027s go."},{"Start":"03:21.470 ","End":"03:24.770","Text":"For fun games, gly,"},{"Start":"03:24.770 ","End":"03:26.300","Text":"hopefully, you remember,"},{"Start":"03:26.300 ","End":"03:27.950","Text":"this stands for glycine,"},{"Start":"03:27.950 ","End":"03:33.740","Text":"pro stands for proline and this 1 that you may not be"},{"Start":"03:33.740 ","End":"03:40.200","Text":"familiar with is actually hydroxyproline."},{"Start":"03:40.200 ","End":"03:42.310","Text":"This is a proline,"},{"Start":"03:42.310 ","End":"03:45.635","Text":"which is formed by hydrolysis of the protein."},{"Start":"03:45.635 ","End":"03:48.700","Text":"Going back and looking at these,"},{"Start":"03:48.700 ","End":"03:51.000","Text":"racing all that I\u0027ve written,"},{"Start":"03:51.000 ","End":"03:56.450","Text":"it\u0027s a repeating tripeptide of gly, x pro,"},{"Start":"03:56.450 ","End":"04:02.494","Text":"and it adopts a left-handed helical structure."},{"Start":"04:02.494 ","End":"04:03.800","Text":"What you see here,"},{"Start":"04:03.800 ","End":"04:07.100","Text":"is the helix goes and turns,"},{"Start":"04:07.100 ","End":"04:09.860","Text":"spirals to the left with 3 residues per turn."},{"Start":"04:09.860 ","End":"04:11.900","Text":"So every turn is 3 residues."},{"Start":"04:11.900 ","End":"04:13.999","Text":"If you see here you see the helix,"},{"Start":"04:13.999 ","End":"04:18.950","Text":"it\u0027s a left-handed helix that\u0027s going like"},{"Start":"04:18.950 ","End":"04:25.745","Text":"this and we said the glycine,"},{"Start":"04:25.745 ","End":"04:31.955","Text":"the x, which could be a various number of residues, and the proline."},{"Start":"04:31.955 ","End":"04:40.160","Text":"This is a left-handed helix structure and it has 3 residues per turn as said,"},{"Start":"04:40.160 ","End":"04:42.919","Text":"gly x and hydroxyproline,"},{"Start":"04:42.919 ","End":"04:51.270","Text":"and 3 of these come together and wrap around 1 another with a right-handed twist."},{"Start":"04:51.270 ","End":"04:54.110","Text":"A right-handed helix."},{"Start":"04:54.110 ","End":"04:57.725","Text":"Now, if before it went left,"},{"Start":"04:57.725 ","End":"04:59.210","Text":"you went left like this."},{"Start":"04:59.210 ","End":"05:01.885","Text":"Now it\u0027s going like this."},{"Start":"05:01.885 ","End":"05:07.415","Text":"You have 3 amino acid residues that come together and form the helix."},{"Start":"05:07.415 ","End":"05:09.650","Text":"3 of these helices come together,"},{"Start":"05:09.650 ","End":"05:14.360","Text":"in a right-handed twist and form this,"},{"Start":"05:14.360 ","End":"05:17.870","Text":"and this comes together to form the collagen fiber."},{"Start":"05:17.870 ","End":"05:19.160","Text":"Now if you look here,"},{"Start":"05:19.160 ","End":"05:26.505","Text":"you actually see the glycine and the proline and whatever you see here."},{"Start":"05:26.505 ","End":"05:28.790","Text":"Again, you have alpha-helices,"},{"Start":"05:28.790 ","End":"05:30.260","Text":"you have 3 of them."},{"Start":"05:30.260 ","End":"05:33.585","Text":"You have 1, 2, 3."},{"Start":"05:33.585 ","End":"05:36.590","Text":"Each one of these is made by"},{"Start":"05:36.590 ","End":"05:40.880","Text":"amino acid sequence that\u0027s made of these 3 amino acid residues."},{"Start":"05:40.880 ","End":"05:44.075","Text":"As you see the amino acid chain here illustrated differently,"},{"Start":"05:44.075 ","End":"05:47.930","Text":"you have this star as the proline."},{"Start":"05:47.930 ","End":"05:51.380","Text":"These blue circles, the glycine,"},{"Start":"05:51.380 ","End":"05:53.285","Text":"and the square is the x,"},{"Start":"05:53.285 ","End":"05:55.115","Text":"is the various amino acid residues."},{"Start":"05:55.115 ","End":"05:58.955","Text":"Now you have the triple helix says of these alpha chains,"},{"Start":"05:58.955 ","End":"06:02.130","Text":"that are each made of triple amino acids."},{"Start":"06:02.130 ","End":"06:06.710","Text":"These come together to form collagen fibrils,"},{"Start":"06:06.710 ","End":"06:09.770","Text":"which come together to form the collagen fibers."},{"Start":"06:09.770 ","End":"06:13.220","Text":"You see here the collagen fibers, that are formed."},{"Start":"06:13.220 ","End":"06:16.264","Text":"Just seeing it differently, again,"},{"Start":"06:16.264 ","End":"06:21.140","Text":"you have the 3 amino acid residues that come together."},{"Start":"06:21.140 ","End":"06:25.355","Text":"Here\u0027s additional figure showing the same thing, different colors."},{"Start":"06:25.355 ","End":"06:27.890","Text":"You\u0027re seeing the same idea."},{"Start":"06:27.890 ","End":"06:34.385","Text":"You have a left-handed helix, alpha-helix that\u0027s left-handed."},{"Start":"06:34.385 ","End":"06:37.970","Text":"You have 3 of these coming together,"},{"Start":"06:37.970 ","End":"06:41.525","Text":"wrap around each other in a right-handed helix,"},{"Start":"06:41.525 ","End":"06:44.660","Text":"this is the left-handed helix."},{"Start":"06:44.660 ","End":"06:51.050","Text":"Right-handed helix is the 3 helices coming together and you see the same here."},{"Start":"06:51.050 ","End":"06:58.660","Text":"These result in creating collagen fibers and you see there are these different colors,"},{"Start":"06:58.660 ","End":"07:00.020","Text":"that are seen here."},{"Start":"07:00.020 ","End":"07:02.315","Text":"It\u0027s emphasized, the striation,"},{"Start":"07:02.315 ","End":"07:04.940","Text":"which can be explained by the fact that"},{"Start":"07:04.940 ","End":"07:08.690","Text":"collagen fibrils are made up of collagen molecules,"},{"Start":"07:08.690 ","End":"07:13.900","Text":"aligned in a staggered fashion and cross-linked."},{"Start":"07:13.940 ","End":"07:16.880","Text":"Here it\u0027s a diner, here it\u0027s a tetramer."},{"Start":"07:16.880 ","End":"07:19.160","Text":"It\u0027s not actually depicting collagen,"},{"Start":"07:19.160 ","End":"07:24.260","Text":"but the idea is that you have helices that can stagger in a range."},{"Start":"07:24.260 ","End":"07:27.315","Text":"When they stagger in a range, as such,"},{"Start":"07:27.315 ","End":"07:32.265","Text":"what you see result is the striation,"},{"Start":"07:32.265 ","End":"07:35.060","Text":"in this coiled sheet and"},{"Start":"07:35.060 ","End":"07:40.685","Text":"this rope-like filament bundle and that\u0027s similar to what happens here."},{"Start":"07:40.685 ","End":"07:43.955","Text":"This striation occurs because there is,"},{"Start":"07:43.955 ","End":"07:47.355","Text":"this staggering of the collagen molecules."},{"Start":"07:47.355 ","End":"07:49.005","Text":"Now the specific alignment,"},{"Start":"07:49.005 ","End":"07:50.590","Text":"and degree of cross-linking,"},{"Start":"07:50.590 ","End":"07:52.520","Text":"vary with the tissue and produce"},{"Start":"07:52.520 ","End":"07:57.815","Text":"characteristic cross striations that can be seen in an electron micrograph."},{"Start":"07:57.815 ","End":"08:01.940","Text":"Every type of secondary structure can be completely described,"},{"Start":"08:01.940 ","End":"08:04.100","Text":"by the bond angles."},{"Start":"08:04.100 ","End":"08:08.265","Text":"You have fine side that we mentioned before each residue."},{"Start":"08:08.265 ","End":"08:12.160","Text":"Just to show a previous image from a previous section,"},{"Start":"08:12.160 ","End":"08:15.250","Text":"these are bond angles,"},{"Start":"08:15.250 ","End":"08:19.415","Text":"and these are used to define secondary structure."},{"Start":"08:19.415 ","End":"08:22.520","Text":"Now when a regular pattern is not found,"},{"Start":"08:22.520 ","End":"08:27.840","Text":"the secondary structure is sometimes referred to as undefined or as a random coil."},{"Start":"08:27.840 ","End":"08:30.500","Text":"We mentioned the alpha helix and we saw that is"},{"Start":"08:30.500 ","End":"08:35.045","Text":"very common as a secondary structure in proteins."},{"Start":"08:35.045 ","End":"08:37.820","Text":"Remember a star peptide is Pauling and Corey,"},{"Start":"08:37.820 ","End":"08:40.385","Text":"they have experimental results of William Astbury,"},{"Start":"08:40.385 ","End":"08:44.570","Text":"who in the 1930s had conducted pioneering X-ray studies of proteins."},{"Start":"08:44.570 ","End":"08:48.920","Text":"Astbury demonstrated that the protein that makes up hair and porcupine quills,"},{"Start":"08:48.920 ","End":"08:52.910","Text":"the fibrous protein is alpha keratin,"},{"Start":"08:52.910 ","End":"08:55.250","Text":"and that is what you see here."},{"Start":"08:55.250 ","End":"09:04.115","Text":"He demonstrated that it has a regular structure that repeats every 5.15-5.2 angstroms."},{"Start":"09:04.115 ","End":"09:13.230","Text":"The angstrom is named after the physicist Anders J. Angstrom is equal to 0.1 nanometers."},{"Start":"09:13.230 ","End":"09:14.890","Text":"Although it\u0027s not an SI unit,"},{"Start":"09:14.890 ","End":"09:19.884","Text":"it is used universally by structural biologist to describe atomic distances."},{"Start":"09:19.884 ","End":"09:22.510","Text":"Now with this information and their data on"},{"Start":"09:22.510 ","End":"09:25.900","Text":"the peptide bond and with the help of precisely constructed models,"},{"Start":"09:25.900 ","End":"09:31.150","Text":"Pauling and Corey set out to determine the likely conformations of protein molecules."},{"Start":"09:31.150 ","End":"09:33.145","Text":"You see alpha keratin here,"},{"Start":"09:33.145 ","End":"09:38.245","Text":"and you see this helical arrangement of 2 of them wrapping around each other."},{"Start":"09:38.245 ","End":"09:41.215","Text":"You see side-chains protruding."},{"Start":"09:41.215 ","End":"09:45.790","Text":"This is the ball and stick 3D figure of this."},{"Start":"09:45.790 ","End":"09:50.260","Text":"Here you also see a different variation."},{"Start":"09:50.260 ","End":"09:54.265","Text":"It\u0027s a helical wheel projection of an alpha helix."},{"Start":"09:54.265 ","End":"10:00.285","Text":"This is the alpha-helix and it\u0027s basically looking at this from the top."},{"Start":"10:00.285 ","End":"10:02.550","Text":"If we\u0027re looking this way in,"},{"Start":"10:02.550 ","End":"10:05.625","Text":"and this representation can be"},{"Start":"10:05.625 ","End":"10:09.650","Text":"colored and used to identify surfaces with specific properties."},{"Start":"10:09.650 ","End":"10:16.560","Text":"For example, the yellow residues could represent hydrophobic residues and could conform,"},{"Start":"10:16.560 ","End":"10:22.250","Text":"so they are away from an aqueous surrounding and aligned next to each other,"},{"Start":"10:22.250 ","End":"10:26.284","Text":"in which case they may want to aggregate with another such interface,"},{"Start":"10:26.284 ","End":"10:30.245","Text":"another hydrophobic surface of a sub-unit or another protein,"},{"Start":"10:30.245 ","End":"10:37.665","Text":"while the red is negative and the blue is a positive charge residue."},{"Start":"10:37.665 ","End":"10:43.055","Text":"These can illustrate potential interaction of opposite charge side-chains,"},{"Start":"10:43.055 ","End":"10:46.415","Text":"separated by 2 residues in the helix."},{"Start":"10:46.415 ","End":"10:50.430","Text":"You can see separation of 2 and 3 before 4,"},{"Start":"10:50.430 ","End":"10:54.420","Text":"5, and 6 if there\u0027s a 7 if it\u0027s 1 of these."},{"Start":"10:54.420 ","End":"10:59.015","Text":"This is a way to actually characterize and"},{"Start":"10:59.015 ","End":"11:03.480","Text":"note and annotate the secondary structure and its properties."},{"Start":"11:03.480 ","End":"11:04.820","Text":"Going back to the alpha helix,"},{"Start":"11:04.820 ","End":"11:06.335","Text":"the simplest arrangement,"},{"Start":"11:06.335 ","End":"11:11.165","Text":"the polypeptide chain could assume with its rigid peptide bonds,"},{"Start":"11:11.165 ","End":"11:15.920","Text":"but other single bonds free to rotate is a helical structure,"},{"Start":"11:15.920 ","End":"11:19.370","Text":"which Pauling and Corey called the alpha helix."},{"Start":"11:19.370 ","End":"11:23.180","Text":"In this structure, the polypeptide backbone is"},{"Start":"11:23.180 ","End":"11:27.680","Text":"tightly wound around an imaginary axis drawn longitudinally through"},{"Start":"11:27.680 ","End":"11:31.680","Text":"the middle of the helix of the amino acid residues and the R groups of"},{"Start":"11:31.680 ","End":"11:35.930","Text":"amino acid residues protrude outward from the helical backbones."},{"Start":"11:35.930 ","End":"11:37.220","Text":"As you see here,"},{"Start":"11:37.220 ","End":"11:41.435","Text":"these are the R groups and they protrude outward."},{"Start":"11:41.435 ","End":"11:45.035","Text":"The repeating sub-unit is a single turn of the helix,"},{"Start":"11:45.035 ","End":"11:50.630","Text":"which extends about 5.4 angstrom along the long axis and it\u0027s slightly greater than"},{"Start":"11:50.630 ","End":"11:56.855","Text":"the periodicity Astbury observed on extra analysis of hair keratin."},{"Start":"11:56.855 ","End":"11:58.070","Text":"When you look at this,"},{"Start":"11:58.070 ","End":"12:00.695","Text":"as it rotates around the axis,"},{"Start":"12:00.695 ","End":"12:04.580","Text":"you see that between the rotations,"},{"Start":"12:04.580 ","End":"12:13.940","Text":"you have about 5.4 angstroms and a distance of about 3.6 residues per rotation."},{"Start":"12:13.940 ","End":"12:20.165","Text":"The alpha-helix confirmations and each helical turn includes 3.6 amino acid residues."},{"Start":"12:20.165 ","End":"12:25.460","Text":"You find that between each helical turn,"},{"Start":"12:25.460 ","End":"12:33.815","Text":"it\u0027s about 5.4 angstrom or 3.6 amino acid residues."},{"Start":"12:33.815 ","End":"12:36.620","Text":"The alpha-helix segments and proteins often"},{"Start":"12:36.620 ","End":"12:39.650","Text":"deviate slightly from these dihedral angles and"},{"Start":"12:39.650 ","End":"12:42.590","Text":"they even vary within a single continuous segment and result"},{"Start":"12:42.590 ","End":"12:45.755","Text":"in subtle bends or kinks in the helical axis."},{"Start":"12:45.755 ","End":"12:50.720","Text":"It\u0027s not necessarily the perfect helix as described or portrayed."},{"Start":"12:50.720 ","End":"12:55.940","Text":"The helical twist of the alpha-helix found in all proteins is right-handed."},{"Start":"12:55.940 ","End":"12:59.900","Text":"Alpha helix proved to be the predominant structure in"},{"Start":"12:59.900 ","End":"13:04.410","Text":"alpha carotenes so just to remind you, right-handed."},{"Start":"13:04.410 ","End":"13:06.285","Text":"More generally, 1/4 of"},{"Start":"13:06.285 ","End":"13:10.985","Text":"all amino acid residues in polypeptides are found in alpha-helices,"},{"Start":"13:10.985 ","End":"13:15.185","Text":"the exact fraction varying greatly from 1 protein to the next."},{"Start":"13:15.185 ","End":"13:18.020","Text":"With this, we completed part 1 of secondary structure,"},{"Start":"13:18.020 ","End":"13:19.550","Text":"where we touched upon"},{"Start":"13:19.550 ","End":"13:23.999","Text":"protein spatial arrangement and alpha-helix conformation orientation."}],"ID":29572},{"Watched":false,"Name":"Secondary Structure Part 2","Duration":"7m 22s","ChapterTopicVideoID":28348,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.725","Text":"Welcome to Part II of the secondary structure within protein structure."},{"Start":"00:04.725 ","End":"00:08.265","Text":"We\u0027re going to continue talking about protein spatial arrangement and"},{"Start":"00:08.265 ","End":"00:12.345","Text":"further dive into Alpha helix conformation and orientation."},{"Start":"00:12.345 ","End":"00:18.090","Text":"Why does the Alpha helix form more readily than many other possible conformations?"},{"Start":"00:18.090 ","End":"00:20.940","Text":"What leads to this reality?"},{"Start":"00:20.940 ","End":"00:27.720","Text":"The answer is in part that an Alpha helix makes optimal use of internal hydrogen bonds."},{"Start":"00:27.720 ","End":"00:31.950","Text":"Here we go, we\u0027re back to these hydrogen bonds that are so important."},{"Start":"00:31.950 ","End":"00:35.100","Text":"The structure is stabilized by a hydrogen bond between"},{"Start":"00:35.100 ","End":"00:39.980","Text":"the hydrogen atom attached to the electronegative nitrogen atom of"},{"Start":"00:39.980 ","End":"00:41.390","Text":"a peptide linkage and"},{"Start":"00:41.390 ","End":"00:44.660","Text":"the electronegative carbonyl oxygen atom of"},{"Start":"00:44.660 ","End":"00:48.875","Text":"the fourth amino acid and the amino terminal side of the peptide bond."},{"Start":"00:48.875 ","End":"00:53.180","Text":"If you have the amino terminal side of the peptide bond,"},{"Start":"00:53.180 ","End":"00:58.125","Text":"you have an electronegative carbonyl oxygen."},{"Start":"00:58.125 ","End":"01:01.159","Text":"When we have an oxygen that\u0027s attached to a carbonyl,"},{"Start":"01:01.159 ","End":"01:05.000","Text":"it will have an electronegative charge."},{"Start":"01:05.000 ","End":"01:10.295","Text":"This will actually interact with"},{"Start":"01:10.295 ","End":"01:18.175","Text":"the hydrogen bond with a positive charge and a hydrogen bond will form."},{"Start":"01:18.175 ","End":"01:20.465","Text":"Within the Alpha helix,"},{"Start":"01:20.465 ","End":"01:23.870","Text":"every peptide bond except those close to"},{"Start":"01:23.870 ","End":"01:28.805","Text":"each end of the helix participates in such hydrogen bonding."},{"Start":"01:28.805 ","End":"01:33.180","Text":"Each successive turn off the Alpha helix is held to adjacent by 3-4 hydrogen bonds."},{"Start":"01:34.450 ","End":"01:38.045","Text":"So you actually see 3-4 hydrogen bonds."},{"Start":"01:38.045 ","End":"01:41.300","Text":"These lines here represent the hydrogen bonding."},{"Start":"01:41.300 ","End":"01:43.250","Text":"You see hydrogen bonding between the positive and the negative."},{"Start":"01:43.250 ","End":"01:52.130","Text":"You see hydrogen bonding again between the positive and the negative, etc."},{"Start":"01:52.130 ","End":"01:58.770","Text":"All the hydrogen bonds combined give the entire helical structure considerable stability."},{"Start":"01:58.770 ","End":"02:05.120","Text":"These hydrogen bonds are what help stabilize this helical structure"},{"Start":"02:05.120 ","End":"02:11.945","Text":"and result in why this Alpha helix is more readily formed than other conformations."},{"Start":"02:11.945 ","End":"02:15.755","Text":"We learned about stereoisomers is optional conformations of proteins can have."},{"Start":"02:15.755 ","End":"02:19.670","Text":"Additional experiments showed that Alpha helixes can form in"},{"Start":"02:19.670 ","End":"02:23.945","Text":"peptides consisting of either L or D amino acids."},{"Start":"02:23.945 ","End":"02:28.535","Text":"However, all residues must be of 1 stereoisomer series."},{"Start":"02:28.535 ","End":"02:30.530","Text":"If D amino acid will disrupt"},{"Start":"02:30.530 ","End":"02:34.465","Text":"a regular structure consisting of L amino acids and vice versa,"},{"Start":"02:34.465 ","End":"02:35.765","Text":"the most stable form,"},{"Start":"02:35.765 ","End":"02:41.390","Text":"an Alpha helix consisting of D amino acids is left-handed but extended left-handed."},{"Start":"02:41.390 ","End":"02:46.810","Text":"Helix is our theoretically less stable and have not been observed in proteins as we said."},{"Start":"02:46.810 ","End":"02:51.345","Text":"In proteins, what is observed as right-handed helixes."},{"Start":"02:51.345 ","End":"02:55.400","Text":"When we\u0027re looking at this helix dipole,"},{"Start":"02:55.400 ","End":"02:59.720","Text":"we\u0027re seeing the electric dipole of a peptide bond and it\u0027s transmitted"},{"Start":"02:59.720 ","End":"03:04.340","Text":"along an Alpha helical segment through the interchain hydrogen bonds."},{"Start":"03:04.340 ","End":"03:08.615","Text":"Again, we\u0027re seeing the hydrogen bonds resulting in an overall helix dipole."},{"Start":"03:08.615 ","End":"03:12.860","Text":"You see partial positive charge here and a partial negative charge"},{"Start":"03:12.860 ","End":"03:17.285","Text":"here so this helix has a partial dipole."},{"Start":"03:17.285 ","End":"03:20.780","Text":"Now in this illustration that amino and carbonyl constituents of"},{"Start":"03:20.780 ","End":"03:25.395","Text":"each peptide bond are indicated by plus and minus."},{"Start":"03:25.395 ","End":"03:33.010","Text":"The amino and carbonyl constituents of each peptide bond are marked by plus or minus"},{"Start":"03:33.010 ","End":"03:34.790","Text":"with the ones grayed out are"},{"Start":"03:34.790 ","End":"03:40.625","Text":"obviously within on the other side of this ribbon that\u0027s representing the helix."},{"Start":"03:40.625 ","End":"03:43.910","Text":"Now, non hydrogen bonded amino and carbonyl constituents in"},{"Start":"03:43.910 ","End":"03:49.430","Text":"the peptide bonds near each end of Alpha helical region are shown in red."},{"Start":"03:49.430 ","End":"03:53.400","Text":"These ones aren\u0027t hydrogen bonded."},{"Start":"03:54.320 ","End":"03:59.120","Text":"You don\u0027t see the hydrogen bond with something else and these"},{"Start":"03:59.120 ","End":"04:03.380","Text":"are what contribute to this dipole."},{"Start":"04:03.380 ","End":"04:05.540","Text":"Going back to the amino acids,"},{"Start":"04:05.540 ","End":"04:09.335","Text":"amino acids sequence affects Alpha helix stability."},{"Start":"04:09.335 ","End":"04:13.310","Text":"Not all polypeptides can form a stable Alpha helix."},{"Start":"04:13.310 ","End":"04:20.165","Text":"Interactions between amino acids side chains can stabilize or destabilize this structure."},{"Start":"04:20.165 ","End":"04:26.705","Text":"For example, if a polypeptide chain has a long block of glue residues,"},{"Start":"04:26.705 ","End":"04:33.850","Text":"this segment of the chain will not form an Alpha helix at pH 7."},{"Start":"04:33.850 ","End":"04:38.810","Text":"The negatively charged carboxyl groups of adjacent\u0027s leucine residues repel"},{"Start":"04:38.810 ","End":"04:43.790","Text":"each other so strongly that they prevent formation of the Alpha helix."},{"Start":"04:43.790 ","End":"04:45.110","Text":"For the same reason,"},{"Start":"04:45.110 ","End":"04:49.670","Text":"if there are many adjacent lysine and or arginine residues"},{"Start":"04:49.670 ","End":"04:52.295","Text":"which have positively charged Arg groups at pH 7,"},{"Start":"04:52.295 ","End":"04:56.900","Text":"they will also repel each other and prevent formation of the Alpha helix."},{"Start":"04:56.900 ","End":"05:00.080","Text":"You have an example of negative charges in"},{"Start":"05:00.080 ","End":"05:04.910","Text":"the glue residues or positive charges in the lysine or arginine residues,"},{"Start":"05:04.910 ","End":"05:08.120","Text":"and these adjacent to each other cause repulsion"},{"Start":"05:08.120 ","End":"05:11.540","Text":"and therefore the Alpha helix is not formed."},{"Start":"05:11.540 ","End":"05:15.200","Text":"Bulk and shape of some residues as well can"},{"Start":"05:15.200 ","End":"05:19.670","Text":"also destabilize an Alpha helix if they are close together in the chain."},{"Start":"05:19.670 ","End":"05:23.555","Text":"Meaning if they\u0027re really big and they take up space,"},{"Start":"05:23.555 ","End":"05:28.205","Text":"the helix can\u0027t form well because there\u0027s some bulky thing in the middle of it."},{"Start":"05:28.205 ","End":"05:29.495","Text":"This can be, for example,"},{"Start":"05:29.495 ","End":"05:32.300","Text":"any of these, you have serine sustain etc."},{"Start":"05:32.300 ","End":"05:37.370","Text":"The twist of an Alpha helix ensures that critical interactions occur between"},{"Start":"05:37.370 ","End":"05:41.700","Text":"an amino acid side chain and the side chain 3"},{"Start":"05:41.700 ","End":"05:46.275","Text":"and sometimes 4 residues away on either side of it."},{"Start":"05:46.275 ","End":"05:50.780","Text":"These interactions can contribute stabilization of the Alpha helix as"},{"Start":"05:50.780 ","End":"05:53.450","Text":"a charged amino acids are often found through residues away from"},{"Start":"05:53.450 ","End":"05:57.080","Text":"negatively charged amino acids permitting the formation of an ion pair."},{"Start":"05:57.080 ","End":"05:59.300","Text":"So 2 aromatic amino acids, for example,"},{"Start":"05:59.300 ","End":"06:03.950","Text":"can also be similarly spaced resulting in a hydrophobic interaction."},{"Start":"06:03.950 ","End":"06:06.785","Text":"Using this example of a figure here,"},{"Start":"06:06.785 ","End":"06:11.680","Text":"interactions between Arg groups of amino acids 3 residues apart and Alpha helix,"},{"Start":"06:11.680 ","End":"06:15.425","Text":"you see an ionic interaction between Asn 100 and"},{"Start":"06:15.425 ","End":"06:20.260","Text":"Arg 103 in an Alpha helical region of the protein."},{"Start":"06:20.260 ","End":"06:23.960","Text":"Basically, we\u0027re seeing a positive charge and"},{"Start":"06:23.960 ","End":"06:27.500","Text":"a negative charge interacting with each other."},{"Start":"06:27.500 ","End":"06:31.325","Text":"As mentioned before, not all polypeptides can form a stable Alpha helix."},{"Start":"06:31.325 ","End":"06:36.350","Text":"The tendency of a given segment of a polypeptide chain to fold up as"},{"Start":"06:36.350 ","End":"06:39.410","Text":"an Alpha helix therefore depends on the identity and"},{"Start":"06:39.410 ","End":"06:43.460","Text":"sequence of the amino acid residues within the segment."},{"Start":"06:43.460 ","End":"06:46.280","Text":"Each amino acid residue and a polypeptide has"},{"Start":"06:46.280 ","End":"06:49.610","Text":"an intrinsic propensity to form an Alpha helix."},{"Start":"06:49.610 ","End":"06:50.930","Text":"Alanine, for example,"},{"Start":"06:50.930 ","End":"06:54.050","Text":"shows the greatest tendency to form Alpha helices."},{"Start":"06:54.050 ","End":"06:56.675","Text":"If you just have a sequence,"},{"Start":"06:56.675 ","End":"06:59.940","Text":"a chain of alanines,"},{"Start":"07:01.040 ","End":"07:07.110","Text":"it will naturally form an Alpha helix."},{"Start":"07:07.110 ","End":"07:08.360","Text":"At this point, we learned about"},{"Start":"07:08.360 ","End":"07:12.185","Text":"proteins spatial arrangement and alpha helix conformation orientation."},{"Start":"07:12.185 ","End":"07:14.955","Text":"We had completed Part II of secondary structure,"},{"Start":"07:14.955 ","End":"07:17.090","Text":"we had talked for the protein spatial arrangement"},{"Start":"07:17.090 ","End":"07:19.085","Text":"and Alpha helix conformation orientation."},{"Start":"07:19.085 ","End":"07:23.550","Text":"We will further delve into us within part 3."}],"ID":29573},{"Watched":false,"Name":"Secondary Structure Part 3","Duration":"9m 52s","ChapterTopicVideoID":28349,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.320","Text":"Welcome back to secondary structure part III within protein structure."},{"Start":"00:04.320 ","End":"00:09.870","Text":"Here we\u0027re going to go into pretty special arrangement and speak about Beta conformation."},{"Start":"00:09.870 ","End":"00:14.925","Text":"The Beta conformation organizes polypeptide chains into sheets."},{"Start":"00:14.925 ","End":"00:18.510","Text":"Protein architecture, the Beta sheets."},{"Start":"00:18.510 ","End":"00:24.014","Text":"In 1951, Pauling and Corey predicted a second type of repetitive structure,"},{"Start":"00:24.014 ","End":"00:30.360","Text":"the Beta conformation, which is a more extended conformation of polypeptide chains."},{"Start":"00:30.360 ","End":"00:34.590","Text":"Its structure has been confirmed by extra analysis and in"},{"Start":"00:34.590 ","End":"00:40.250","Text":"the Beta conformation the backbone of the polypeptide chain"},{"Start":"00:40.250 ","End":"00:42.890","Text":"is also defined by atoms arranged according to"},{"Start":"00:42.890 ","End":"00:46.040","Text":"characteristic set of dihedral angles which results in"},{"Start":"00:46.040 ","End":"00:52.395","Text":"an extended zigzag formation rather than a helical structure."},{"Start":"00:52.395 ","End":"00:54.935","Text":"What you see here, basically,"},{"Start":"00:54.935 ","End":"01:01.300","Text":"you have a zigzag formation while you have spiral for Alpha-helix,"},{"Start":"01:01.300 ","End":"01:05.890","Text":"a helical formation, here you have a zigzag formation."},{"Start":"01:05.890 ","End":"01:10.190","Text":"The arrangement of several such zigzag segments side-by-side,"},{"Start":"01:10.190 ","End":"01:13.955","Text":"all which are in the Beta conformation is called"},{"Start":"01:13.955 ","End":"01:18.545","Text":"the Beta sheet and has a pleated appearance."},{"Start":"01:18.545 ","End":"01:21.320","Text":"Hydrogen bonds are formed between"},{"Start":"01:21.320 ","End":"01:24.665","Text":"these adjacent segments of polypeptide chains in the Beta sheet."},{"Start":"01:24.665 ","End":"01:26.420","Text":"The individual segments that form"},{"Start":"01:26.420 ","End":"01:29.975","Text":"a Beta sheet are usually nearby on the polypeptide chain,"},{"Start":"01:29.975 ","End":"01:36.140","Text":"but can also be quite distant from each other in the linear sequence of the polypeptide."},{"Start":"01:36.140 ","End":"01:40.685","Text":"They may even be segments in different polypeptide chains."},{"Start":"01:40.685 ","End":"01:44.420","Text":"The R groups of adjacent amino acids protrude from"},{"Start":"01:44.420 ","End":"01:47.975","Text":"the zigzag structure in opposite directions,"},{"Start":"01:47.975 ","End":"01:52.775","Text":"creating the alternating pattern seen in the side views."},{"Start":"01:52.775 ","End":"02:00.045","Text":"You have them going onto one direction and the next one going the other direction."},{"Start":"02:00.045 ","End":"02:05.885","Text":"As you see, they just move from one direction to the other, opposing directions."},{"Start":"02:05.885 ","End":"02:11.509","Text":"Now these top and side views reveal the R groups extending out from"},{"Start":"02:11.509 ","End":"02:13.880","Text":"the Beta sheets and emphasize"},{"Start":"02:13.880 ","End":"02:17.030","Text":"the pleated shape described as the planes of the peptide bonds."},{"Start":"02:17.030 ","End":"02:23.255","Text":"An alternative name for this structure is the Beta pleated sheet."},{"Start":"02:23.255 ","End":"02:28.865","Text":"Hydrogen bonds cross-link between adjacent chains are also shown."},{"Start":"02:28.865 ","End":"02:33.949","Text":"You see the hydrogen bonds between these adjacent chains."},{"Start":"02:33.949 ","End":"02:40.040","Text":"The adjacent polypeptide chains in Beta sheets can be either parallel or anti-parallel,"},{"Start":"02:40.040 ","End":"02:45.845","Text":"having the same or opposite amino to carboxyl orientations respectively."},{"Start":"02:45.845 ","End":"02:53.850","Text":"If it\u0027s parallel, you have the same amino to carboxyl orientation as seen in this figure."},{"Start":"02:53.850 ","End":"02:59.195","Text":"The antiparallel are when it\u0027s opposite amino to carboxyl orientation."},{"Start":"02:59.195 ","End":"03:01.010","Text":"Now the structures are somewhat similar,"},{"Start":"03:01.010 ","End":"03:04.640","Text":"although the repeat period is shorter for the parallel confirmation,"},{"Start":"03:04.640 ","End":"03:10.175","Text":"it\u0027s closer, 6.5 strong versus 7 for anti-parallel,"},{"Start":"03:10.175 ","End":"03:12.739","Text":"and the hydrogen bonding patterns are different."},{"Start":"03:12.739 ","End":"03:16.805","Text":"If you see the hydrogen bondings in the antiparallel versus the parallel,"},{"Start":"03:16.805 ","End":"03:20.180","Text":"you see the blue lines that we see."},{"Start":"03:20.180 ","End":"03:23.420","Text":"Those blue lines that indicate hydrogen bonds,"},{"Start":"03:23.420 ","End":"03:28.415","Text":"they are different between the 2 different types of Beta sheets."},{"Start":"03:28.415 ","End":"03:32.668","Text":"The inner strand hydrogen bonds are essentially an anti-parallel Beta sheets,"},{"Start":"03:32.668 ","End":"03:33.950","Text":"it seems like they\u0027re in line,"},{"Start":"03:33.950 ","End":"03:38.735","Text":"whereas they\u0027re distorted or not in line for the parallel variant,"},{"Start":"03:38.735 ","End":"03:43.445","Text":"meaning they\u0027re diagonal and doesn\u0027t seem like they\u0027re in line one with the other."},{"Start":"03:43.445 ","End":"03:49.995","Text":"Some proteins structures limit the amino acids that can occur in the Beta sheet."},{"Start":"03:49.995 ","End":"03:54.290","Text":"When 2 or more Beta sheets are layered close together within a protein,"},{"Start":"03:54.290 ","End":"03:57.320","Text":"the R groups of the amino acid residues on"},{"Start":"03:57.320 ","End":"04:00.980","Text":"the touching surfaces must be relatively small."},{"Start":"04:00.980 ","End":"04:02.015","Text":"If they are big,"},{"Start":"04:02.015 ","End":"04:04.070","Text":"it disrupts this and therefore,"},{"Start":"04:04.070 ","End":"04:07.265","Text":"it can\u0027t be layered close together."},{"Start":"04:07.265 ","End":"04:10.775","Text":"Beta-keratin such as fibroin and the fibroin of"},{"Start":"04:10.775 ","End":"04:16.948","Text":"spider webs have a very high content of glycine and alanine residues,"},{"Start":"04:16.948 ","End":"04:20.240","Text":"the 2 amino acids with the smallest R groups,"},{"Start":"04:20.240 ","End":"04:23.060","Text":"the smallest side chains and in silk fibroin and"},{"Start":"04:23.060 ","End":"04:26.960","Text":"glycine and alanine alternate over large parts of the sequence."},{"Start":"04:26.960 ","End":"04:30.605","Text":"Beta-turns are common in proteins."},{"Start":"04:30.605 ","End":"04:36.095","Text":"We mentioned this is another option from Alpha helixes and Beta sheets."},{"Start":"04:36.095 ","End":"04:39.966","Text":"In globular proteins which have a compact folded structure,"},{"Start":"04:39.966 ","End":"04:45.499","Text":"these proteins are known and characterized by being a small bundle."},{"Start":"04:45.499 ","End":"04:48.770","Text":"Nearly 1/3 of the amino acid residues are in"},{"Start":"04:48.770 ","End":"04:52.850","Text":"turns or loops where the polypeptide chain reverses directions."},{"Start":"04:52.850 ","End":"04:56.120","Text":"If you see here, there\u0027s a reverse of direction."},{"Start":"04:56.120 ","End":"04:59.630","Text":"These are the connecting elements that link successive runs"},{"Start":"04:59.630 ","End":"05:03.696","Text":"of Alpha helix or Beta conformation, Beta sheets."},{"Start":"05:03.696 ","End":"05:07.850","Text":"Particularly common are Beta-turns that connect the end of"},{"Start":"05:07.850 ","End":"05:12.350","Text":"2 adjacent segments of anti-parallel Beta sheets."},{"Start":"05:12.350 ","End":"05:19.855","Text":"The structure is a 180 degree turn involving 4 amino acid residues with"},{"Start":"05:19.855 ","End":"05:22.640","Text":"the carbonyl oxygen of the first residue forming"},{"Start":"05:22.640 ","End":"05:27.440","Text":"a hydrogen bond with the amino group hydrogen of the fourth."},{"Start":"05:27.440 ","End":"05:29.330","Text":"The peptide groups of"},{"Start":"05:29.330 ","End":"05:35.072","Text":"the 2 central residues do not participate in any inter-residue hydrogen bonding,"},{"Start":"05:35.072 ","End":"05:38.885","Text":"but you see the hydrogen bond here between"},{"Start":"05:38.885 ","End":"05:44.630","Text":"the oxygen of the first residue and the hydrogen of the fourth residue."},{"Start":"05:44.630 ","End":"05:46.430","Text":"You see that here as well."},{"Start":"05:46.430 ","End":"05:51.140","Text":"There are the 2 types of Beta-turns and the oxygen of"},{"Start":"05:51.140 ","End":"05:56.735","Text":"the first residue is hydrogen bonding with the hydrogen of the fourth residue."},{"Start":"05:56.735 ","End":"06:00.770","Text":"Glycine and proline residues often occur in Beta-turns."},{"Start":"06:00.770 ","End":"06:02.930","Text":"As you see here, this is a proline,"},{"Start":"06:02.930 ","End":"06:04.392","Text":"this is a glycine,"},{"Start":"06:04.392 ","End":"06:06.317","Text":"this we\u0027re talking about the glycine,"},{"Start":"06:06.317 ","End":"06:10.250","Text":"it\u0027s non flexible with the latter because peptide bonds"},{"Start":"06:10.250 ","End":"06:15.320","Text":"involving the amino nitrogen proline readily assume the cis configuration,"},{"Start":"06:15.320 ","End":"06:20.210","Text":"which is a form that is particularly amenable to a right turn."},{"Start":"06:20.210 ","End":"06:24.995","Text":"Amino group is a molecule with both amine, SNNH."},{"Start":"06:24.995 ","End":"06:28.858","Text":"You have the CN, and NH,"},{"Start":"06:28.858 ","End":"06:34.775","Text":"and a carboxylic, a COOH functional groups attached to the same carbon atom."},{"Start":"06:34.775 ","End":"06:39.973","Text":"Amino acids containing a secondary amine group are sometimes named imino acids,"},{"Start":"06:39.973 ","End":"06:45.585","Text":"for example, proline, so imino acid."},{"Start":"06:45.585 ","End":"06:47.810","Text":"Of the several Beta-turns,"},{"Start":"06:47.810 ","End":"06:52.325","Text":"these 2 that are shown here are the most common,"},{"Start":"06:52.325 ","End":"06:55.655","Text":"type I Beta-turn and type II Beta-turn."},{"Start":"06:55.655 ","End":"07:00.440","Text":"What you see in type I is there\u0027s a prolene involved and you have this going around."},{"Start":"07:00.440 ","End":"07:03.785","Text":"This type II, glycine is used."},{"Start":"07:03.785 ","End":"07:08.175","Text":"Now, type I and type II that are the most common."},{"Start":"07:08.175 ","End":"07:12.680","Text":"Type I still occurs more than twice as frequently as type II."},{"Start":"07:12.680 ","End":"07:16.655","Text":"Type II Beta-turns always have glycine as the third residue."},{"Start":"07:16.655 ","End":"07:19.730","Text":"Note the hydrogen bond between the peptide group,"},{"Start":"07:19.730 ","End":"07:21.860","Text":"first and fourth residues of the bonds."},{"Start":"07:21.860 ","End":"07:26.450","Text":"Individual amino acid residues are framed by large blue circles,"},{"Start":"07:26.450 ","End":"07:33.260","Text":"and the individual amino acids are framed by these large blue circles and numbered."},{"Start":"07:33.260 ","End":"07:36.950","Text":"As I mentioned, you have these 4 and they circle and they have"},{"Start":"07:36.950 ","End":"07:43.080","Text":"this 180 degree turn involving these 4 amino acid residue."},{"Start":"07:43.080 ","End":"07:47.210","Text":"Beta-turns are often found near the surface of a protein where"},{"Start":"07:47.210 ","End":"07:52.505","Text":"the peptide groups of the central 2 amino acid residues can hydrogen bond with water."},{"Start":"07:52.505 ","End":"07:57.740","Text":"Remember, we mentioned the tern that these central 2 don\u0027t form"},{"Start":"07:57.740 ","End":"08:04.025","Text":"hydrogen bonds with each other and they are left to be able to hydrogen bond with water."},{"Start":"08:04.025 ","End":"08:06.341","Text":"The Gamma-turn is less common,"},{"Start":"08:06.341 ","End":"08:11.465","Text":"it\u0027s a 3 residue turn with a hydrogen bond between the first and third residues."},{"Start":"08:11.465 ","End":"08:16.849","Text":"The only amino acid residue often found in confirmation outside these regions is glycine."},{"Start":"08:16.849 ","End":"08:18.140","Text":"Because its side chain,"},{"Start":"08:18.140 ","End":"08:20.450","Text":"it\u0027s single hydrogen atom, is small,"},{"Start":"08:20.450 ","End":"08:22.040","Text":"a glycine residue can take part in"},{"Start":"08:22.040 ","End":"08:25.600","Text":"many conformations that are sterically forbidden for other amino acids."},{"Start":"08:25.600 ","End":"08:27.920","Text":"Amino acids are accommodated better than others"},{"Start":"08:27.920 ","End":"08:30.095","Text":"in the different types of secondary structures."},{"Start":"08:30.095 ","End":"08:34.400","Text":"Biases such as the common presence of proline and glycine residues in Beta-turns and"},{"Start":"08:34.400 ","End":"08:37.340","Text":"their relative absences in Alpha-helices are"},{"Start":"08:37.340 ","End":"08:40.990","Text":"readily explained by the known constraints on the different secondary structures."},{"Start":"08:40.990 ","End":"08:43.580","Text":"Other evident biases may be explained by taking into"},{"Start":"08:43.580 ","End":"08:46.145","Text":"account the sizes of charges of side-chains,"},{"Start":"08:46.145 ","End":"08:48.650","Text":"but not all the turns are understood."},{"Start":"08:48.650 ","End":"08:53.290","Text":"We know that there\u0027s a matter of size, charge,"},{"Start":"08:53.290 ","End":"08:56.980","Text":"etc and these characteristics"},{"Start":"08:56.980 ","End":"09:03.670","Text":"contribute to the formation and the stabilization of the secondary structure."},{"Start":"09:03.670 ","End":"09:07.040","Text":"If we summarize protein\u0027s secondary structure,"},{"Start":"09:07.040 ","End":"09:10.610","Text":"secondary structure can be defined as the spatial arrangement of"},{"Start":"09:10.610 ","End":"09:14.705","Text":"amino acid residues that are adjacent in the primary structure."},{"Start":"09:14.705 ","End":"09:17.990","Text":"The most common secondary structure is"},{"Start":"09:17.990 ","End":"09:23.110","Text":"the Alpha-helix and the Beta conformation and, Beta-turns."},{"Start":"09:23.110 ","End":"09:28.070","Text":"The secondary structure of a polypeptide segment can be completely defined if"},{"Start":"09:28.070 ","End":"09:33.860","Text":"the Phi and Psi angles are known for all amino acid residues in that segment,"},{"Start":"09:33.860 ","End":"09:36.019","Text":"and therefore, it can be predicted."},{"Start":"09:36.019 ","End":"09:41.240","Text":"With this, we completed part B where we introduced Beta conformation and completed"},{"Start":"09:41.240 ","End":"09:44.570","Text":"the entire section of protein structure"},{"Start":"09:44.570 ","End":"09:47.960","Text":"with all 3 parts where we talked about protein spatial arrangement,"},{"Start":"09:47.960 ","End":"09:52.290","Text":"Alpha-helix conformation orientation, and Beta conformation."}],"ID":29574},{"Watched":false,"Name":"Exercise 1","Duration":"44s","ChapterTopicVideoID":28350,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.150","Text":"Upon completion of the lesson on secondary structure,"},{"Start":"00:03.150 ","End":"00:04.950","Text":"let\u0027s start with exercise."},{"Start":"00:04.950 ","End":"00:09.405","Text":"Explain what the term secondary structure refers to in a protein."},{"Start":"00:09.405 ","End":"00:13.470","Text":"The term secondary structure refers to any chosen segment of"},{"Start":"00:13.470 ","End":"00:19.005","Text":"a polypeptide chain and describes the local spatial arrangement of its main chain atom."},{"Start":"00:19.005 ","End":"00:23.415","Text":"This is without regard to its side chains or its relationship to other segments."},{"Start":"00:23.415 ","End":"00:26.820","Text":"The discussion of secondary structure mostly focuses on"},{"Start":"00:26.820 ","End":"00:30.795","Text":"common regular folding patterns of the polypeptide backbone."},{"Start":"00:30.795 ","End":"00:36.230","Text":"A few types of secondary structure are particularly stable and occur widely in proteins,"},{"Start":"00:36.230 ","End":"00:40.565","Text":"the most prominent are the Alpha helix and Beta conformations."},{"Start":"00:40.565 ","End":"00:44.400","Text":"We also mentioned Beta turns."}],"ID":29575},{"Watched":false,"Name":"Exercise 2","Duration":"2m 31s","ChapterTopicVideoID":28351,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.580","Text":"Let\u0027s test your knowledge further about protein secondary structure."},{"Start":"00:05.580 ","End":"00:08.760","Text":"Which statement is false and why?"},{"Start":"00:08.760 ","End":"00:11.250","Text":"A, Pauling and Corey,"},{"Start":"00:11.250 ","End":"00:13.440","Text":"where scientists that studied peptides and that"},{"Start":"00:13.440 ","End":"00:17.130","Text":"predicted the existence of protein secondary structures."},{"Start":"00:17.130 ","End":"00:22.509","Text":"B, common secondary structures have characteristic bond angles and amino acid content."},{"Start":"00:22.509 ","End":"00:25.530","Text":"C, the Alpha helix and Beta conformation are"},{"Start":"00:25.530 ","End":"00:29.520","Text":"the major repetitive secondary structures in a wide variety of proteins."},{"Start":"00:29.520 ","End":"00:35.130","Text":"D, other repetitive structures exist in some specialized proteins and E,"},{"Start":"00:35.130 ","End":"00:37.050","Text":"some secondary structures can be described by"},{"Start":"00:37.050 ","End":"00:40.050","Text":"the bond angles of Phi and Psi at each residue."},{"Start":"00:40.050 ","End":"00:41.580","Text":"Let\u0027s start with A."},{"Start":"00:41.580 ","End":"00:43.550","Text":"We\u0027re looking for what\u0027s false."},{"Start":"00:43.550 ","End":"00:48.320","Text":"We mentioned Pauling and Corey a few times as scientists that studied"},{"Start":"00:48.320 ","End":"00:50.990","Text":"peptide and peptide bonds and they did"},{"Start":"00:50.990 ","End":"00:54.260","Text":"predict the existence of protein secondary structures."},{"Start":"00:54.260 ","End":"01:01.745","Text":"They study this in late 1930s and they came up with evidence also in 1951."},{"Start":"01:01.745 ","End":"01:03.770","Text":"This seems true, therefore,"},{"Start":"01:03.770 ","End":"01:07.595","Text":"this is not our answer as we\u0027re looking for what\u0027s false."},{"Start":"01:07.595 ","End":"01:12.860","Text":"B, common secondary structures have characteristic bond angles and amino acid content."},{"Start":"01:12.860 ","End":"01:14.885","Text":"Well, we know this is true."},{"Start":"01:14.885 ","End":"01:16.730","Text":"There are common secondary structures."},{"Start":"01:16.730 ","End":"01:17.810","Text":"We talked about them."},{"Start":"01:17.810 ","End":"01:20.630","Text":"They tend to have characteristic bond angles,"},{"Start":"01:20.630 ","End":"01:24.440","Text":"we talked about the Alpha helix. We mentioned."},{"Start":"01:24.440 ","End":"01:30.600","Text":"They also have specific or typical amino acid contents."},{"Start":"01:30.600 ","End":"01:33.200","Text":"This seems like a true statement, therefore,"},{"Start":"01:33.200 ","End":"01:36.769","Text":"it can\u0027t be our correct answer as being false."},{"Start":"01:36.769 ","End":"01:39.770","Text":"C, the Alpha helix and Beta conformation are"},{"Start":"01:39.770 ","End":"01:43.670","Text":"the major repetitive secondary structures in a wide variety of proteins."},{"Start":"01:43.670 ","End":"01:47.660","Text":"Yes, we said these are the most common."},{"Start":"01:47.660 ","End":"01:50.075","Text":"We also mentioned the Beta turns,"},{"Start":"01:50.075 ","End":"01:54.335","Text":"but these are less common than the Alpha helices and Beta conformations."},{"Start":"01:54.335 ","End":"01:56.345","Text":"Again, C is true,"},{"Start":"01:56.345 ","End":"01:57.860","Text":"therefore it\u0027s not our answer."},{"Start":"01:57.860 ","End":"02:00.590","Text":"D, other repetitive structures then"},{"Start":"02:00.590 ","End":"02:04.625","Text":"the Alpha helix and Beta conformation exist in some specialized proteins."},{"Start":"02:04.625 ","End":"02:08.420","Text":"We also mentioned this and we gave an example in contexts of collagen,"},{"Start":"02:08.420 ","End":"02:11.780","Text":"and therefore this is true and it leaves us with"},{"Start":"02:11.780 ","End":"02:15.320","Text":"E. Let\u0027s go over this and see if this is false."},{"Start":"02:15.320 ","End":"02:17.960","Text":"E, some secondary structures can be"},{"Start":"02:17.960 ","End":"02:20.980","Text":"described by the bond angles of Phi and Psi at each residue."},{"Start":"02:20.980 ","End":"02:22.410","Text":"To make it true,"},{"Start":"02:22.410 ","End":"02:26.000","Text":"we can say every type of secondary structure can be completely described"},{"Start":"02:26.000 ","End":"02:30.720","Text":"by the bond angles Phi and Psi at each residue."}],"ID":29576},{"Watched":false,"Name":"Exercise 3","Duration":"1m 42s","ChapterTopicVideoID":28352,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.120","Text":"What did we learn about protein secondary structure?"},{"Start":"00:03.120 ","End":"00:06.310","Text":"What is the simplest arrangement a polypeptide chain could assume,"},{"Start":"00:06.310 ","End":"00:08.325","Text":"and what is it specifically called?"},{"Start":"00:08.325 ","End":"00:12.855","Text":"The simplest arrangement a polypeptide can assume is a helical one,"},{"Start":"00:12.855 ","End":"00:18.435","Text":"and it is called the Alpha helix. Part 2."},{"Start":"00:18.435 ","End":"00:21.545","Text":"Mention 2 characteristics of this arrangement."},{"Start":"00:21.545 ","End":"00:25.220","Text":"We mentioned a few more than 2 during the lesson,"},{"Start":"00:25.220 ","End":"00:29.765","Text":"so whichever 2 you decide to, we\u0027re good with that."},{"Start":"00:29.765 ","End":"00:34.310","Text":"The Alpha helix arrangement is 1 in which the polypeptide backbone is"},{"Start":"00:34.310 ","End":"00:36.770","Text":"tightly wound around an imaginary axis"},{"Start":"00:36.770 ","End":"00:39.590","Text":"drawn longitudinally through the middle of the helix,"},{"Start":"00:39.590 ","End":"00:45.109","Text":"and the R groups of amino acid residues protrude outward from the helical backbone."},{"Start":"00:45.109 ","End":"00:49.640","Text":"Furthermore, the repeating unit in this structure is a single turn of the helix,"},{"Start":"00:49.640 ","End":"00:54.025","Text":"which extends about 5.4 angstrom along the long axis."},{"Start":"00:54.025 ","End":"00:56.645","Text":"Now, if all of this sounds like Chinese to you,"},{"Start":"00:56.645 ","End":"00:59.540","Text":"go back to the lesson and look at the figures."},{"Start":"00:59.540 ","End":"01:01.070","Text":"The Alpha helix is 1 of"},{"Start":"01:01.070 ","End":"01:06.140","Text":"the 2 major repetitive secondary structures present in a wide variety of proteins."},{"Start":"01:06.140 ","End":"01:08.080","Text":"Do you remember what the second one is?"},{"Start":"01:08.080 ","End":"01:09.845","Text":"Generally, about 1/4 of"},{"Start":"01:09.845 ","End":"01:14.270","Text":"all amino acid residues in polypeptides are found in Alpha helices."},{"Start":"01:14.270 ","End":"01:19.069","Text":"The exact fraction varying greatly from 1 protein to the next."},{"Start":"01:19.069 ","End":"01:23.885","Text":"As already mentioned, any of these things we covered in the lesson can be mentioned,"},{"Start":"01:23.885 ","End":"01:27.395","Text":"and I just mentioned a couple of examples or few examples."},{"Start":"01:27.395 ","End":"01:28.730","Text":"These are not the only ones."},{"Start":"01:28.730 ","End":"01:32.170","Text":"We included a lot more information about this arrangement."},{"Start":"01:32.170 ","End":"01:36.680","Text":"If you didn\u0027t mention 1 of these and mentioned 2 other things"},{"Start":"01:36.680 ","End":"01:42.270","Text":"that you verify that are correct from the lesson, that is fine."}],"ID":29577},{"Watched":false,"Name":"Exercise 4","Duration":"1m 42s","ChapterTopicVideoID":28353,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.975","Text":"Welcome to another exercise covering protein secondary structure."},{"Start":"00:03.975 ","End":"00:08.560","Text":"Why does the Alpha helix form more readily than many other possible conformations,"},{"Start":"00:08.560 ","End":"00:12.915","Text":"and approximately what portion of amino acid residues are found in such arrangements?"},{"Start":"00:12.915 ","End":"00:14.220","Text":"Generally about 1/4 of"},{"Start":"00:14.220 ","End":"00:17.400","Text":"all amino acid residues in polypeptides are found in Alpha-helices."},{"Start":"00:17.400 ","End":"00:19.455","Text":"We just mentioned this in the previous exercise,"},{"Start":"00:19.455 ","End":"00:23.270","Text":"with exact fraction varying greatly from 1 protein to the next."},{"Start":"00:23.270 ","End":"00:25.730","Text":"The Alpha helix forms more readily than"},{"Start":"00:25.730 ","End":"00:28.370","Text":"many other possible conformations in part because"},{"Start":"00:28.370 ","End":"00:31.160","Text":"it makes optimally use of internal hydrogen bonds."},{"Start":"00:31.160 ","End":"00:33.940","Text":"We\u0027ve talked about those hydrogen bonds being important again."},{"Start":"00:33.940 ","End":"00:36.680","Text":"The structure is stabilized by a hydrogen bond between"},{"Start":"00:36.680 ","End":"00:40.430","Text":"the hydrogen atom attached to the electronegative nitrogen atom of"},{"Start":"00:40.430 ","End":"00:42.210","Text":"a peptide linkage and"},{"Start":"00:42.210 ","End":"00:45.350","Text":"the electronegative carbonyl oxygen atom of"},{"Start":"00:45.350 ","End":"00:48.890","Text":"the fourth amino acid on the amino terminal side of that peptide bonds."},{"Start":"00:48.890 ","End":"00:51.380","Text":"Remember we\u0027ve talked about the hydrogen bond between"},{"Start":"00:51.380 ","End":"00:54.934","Text":"the hydrogen atom that\u0027s attached to the electronegative nitrogen"},{"Start":"00:54.934 ","End":"00:57.950","Text":"and the electronegative carbonyl oxygen atom of"},{"Start":"00:57.950 ","End":"01:01.780","Text":"the fourth amino acid on the amino terminal side of a peptide bond."},{"Start":"01:01.780 ","End":"01:03.470","Text":"Within the Alpha helix,"},{"Start":"01:03.470 ","End":"01:07.265","Text":"every peptide bond except those close to each end of the helix,"},{"Start":"01:07.265 ","End":"01:10.745","Text":"participates in such hydrogen bonding."},{"Start":"01:10.745 ","End":"01:16.195","Text":"Each successive turn off the Alpha helix is held adjacent turns by 3-4 hydrogen bonds."},{"Start":"01:16.195 ","End":"01:20.705","Text":"These internal inherent hydrogen bonding capabilities"},{"Start":"01:20.705 ","End":"01:26.240","Text":"stabilize these Alpha helices and also allow the confirmation to happen."},{"Start":"01:26.240 ","End":"01:29.300","Text":"All the hydrogen bonds combined give the entire helical"},{"Start":"01:29.300 ","End":"01:32.780","Text":"structure considerable stability, and with that,"},{"Start":"01:32.780 ","End":"01:36.950","Text":"we have why these are stable and are"},{"Start":"01:36.950 ","End":"01:42.630","Text":"found more commonly and how these conformations are possible."}],"ID":29578},{"Watched":false,"Name":"Exercise 5","Duration":"1m 14s","ChapterTopicVideoID":28354,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.515","Text":"We\u0027re going to have another exercise within secondary structure of proteins."},{"Start":"00:04.515 ","End":"00:06.810","Text":"What can be said about the Alpha helix with regard to"},{"Start":"00:06.810 ","End":"00:11.205","Text":"stereoisomers and L or D amino acids?"},{"Start":"00:11.205 ","End":"00:15.570","Text":"Connecting a topic we covered in an earlier lesson about stereoisomers which can be"},{"Start":"00:15.570 ","End":"00:19.965","Text":"described as the optimal conformations a protein can have in relation to Alpha helices,"},{"Start":"00:19.965 ","End":"00:23.130","Text":"experiments showed that Alpha helices can form in"},{"Start":"00:23.130 ","End":"00:26.775","Text":"peptides consisting of either L or D-amino acids."},{"Start":"00:26.775 ","End":"00:33.075","Text":"However, all residues must be of 1 stereoisomeric series. What does this mean?"},{"Start":"00:33.075 ","End":"00:35.600","Text":"A D-amino acid will disrupt a regular structure"},{"Start":"00:35.600 ","End":"00:38.485","Text":"consisting of L-amino acids and vice versa."},{"Start":"00:38.485 ","End":"00:42.110","Text":"You can\u0027t have a D-amino acid and then an L-amino acid then a D, no,"},{"Start":"00:42.110 ","End":"00:46.670","Text":"it has to be a chain of D-amino acids or a chain of L-amino acids."},{"Start":"00:46.670 ","End":"00:51.635","Text":"The most stable form of an Alpha helix consisting of D-amino acids is left-handed,"},{"Start":"00:51.635 ","End":"00:57.500","Text":"but we\u0027ve mentioned that proteins found are right-handed helices."},{"Start":"00:57.500 ","End":"01:01.460","Text":"Going to say, extended left-handed helices are"},{"Start":"01:01.460 ","End":"01:05.765","Text":"theoretically less stable and have not been observed in proteins."},{"Start":"01:05.765 ","End":"01:07.534","Text":"Though this is possible,"},{"Start":"01:07.534 ","End":"01:14.040","Text":"it hasn\u0027t been found to actually occur in proteins naturally."}],"ID":29579},{"Watched":false,"Name":"Exercise 6","Duration":"2m 50s","ChapterTopicVideoID":28355,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.590 ","End":"00:05.610","Text":"We have another question to tackle within secondary structures of proteins."},{"Start":"00:05.610 ","End":"00:08.820","Text":"Explain this statement and elaborate, give examples."},{"Start":"00:08.820 ","End":"00:12.899","Text":"Amino acid sequence affects Alpha helix stability."},{"Start":"00:12.899 ","End":"00:18.855","Text":"Well, not all polypeptides can form a stable Alpha helix."},{"Start":"00:18.855 ","End":"00:26.345","Text":"Interactions between amino acid side chains can stabilize or destabilize the structure."},{"Start":"00:26.345 ","End":"00:29.830","Text":"An examples of such cases; A,"},{"Start":"00:29.830 ","End":"00:35.000","Text":"a polypeptide chain with a long block of glycine residues will not form"},{"Start":"00:35.000 ","End":"00:41.720","Text":"an Alpha helix at pH 7 because at that particular segment of the polypeptide chain,"},{"Start":"00:41.720 ","End":"00:45.755","Text":"because the negatively charged carboxyl groups of adjacent Glu residues"},{"Start":"00:45.755 ","End":"00:51.400","Text":"repel each other so strongly that they prevent formation of the Alpha helix."},{"Start":"00:51.400 ","End":"00:52.760","Text":"B, if there are"},{"Start":"00:52.760 ","End":"00:55.550","Text":"many adjacent lysine and or arginine residues"},{"Start":"00:55.550 ","End":"00:58.520","Text":"which have positively charged R groups at pH 7,"},{"Start":"00:58.520 ","End":"01:02.675","Text":"they will also repel each other and prevent formation of the Alpha helix."},{"Start":"01:02.675 ","End":"01:07.160","Text":"We have examples of the negatively charged residues"},{"Start":"01:07.160 ","End":"01:11.600","Text":"that if they\u0027re adjacent repel each other and the helix doesn\u0027t form."},{"Start":"01:11.600 ","End":"01:17.675","Text":"Or if you have positively charged R group side chains adjacent to each other,"},{"Start":"01:17.675 ","End":"01:22.355","Text":"they also will repel each other and prevent the formation of the Alpha helix."},{"Start":"01:22.355 ","End":"01:27.820","Text":"C, the bulk and shape of some residues such as Ser and Cys,"},{"Start":"01:27.820 ","End":"01:31.720","Text":"and we mentioned a couple of more aside from serine and cysteine,"},{"Start":"01:31.720 ","End":"01:38.840","Text":"can also destabilize an Alpha helix if they are close to each other in the chain."},{"Start":"01:38.840 ","End":"01:42.575","Text":"They\u0027re close together because they are big and bulky,"},{"Start":"01:42.575 ","End":"01:46.890","Text":"it can destruct because there\u0027s this big side chain."},{"Start":"01:46.890 ","End":"01:49.715","Text":"If you\u0027re holding this huge couch in front of you,"},{"Start":"01:49.715 ","End":"01:52.400","Text":"a person in front of you can\u0027t get too close to you."},{"Start":"01:52.400 ","End":"01:54.200","Text":"This is giving examples of"},{"Start":"01:54.200 ","End":"02:00.020","Text":"how amino acid side chains or residues can affect the structure."},{"Start":"02:00.020 ","End":"02:05.630","Text":"Going back to the idea that not all polypeptides can form a stable Alpha helix,"},{"Start":"02:05.630 ","End":"02:10.940","Text":"the tendency of a given segment of a polypeptide chain to fold up as"},{"Start":"02:10.940 ","End":"02:13.900","Text":"an Alpha helix therefore depends on the identity"},{"Start":"02:13.900 ","End":"02:17.330","Text":"and sequence of amino acid residues within the segment."},{"Start":"02:17.330 ","End":"02:20.390","Text":"Each amino acid residue in a polypeptide has"},{"Start":"02:20.390 ","End":"02:24.055","Text":"an intrinsic propensity to form an Alpha helix."},{"Start":"02:24.055 ","End":"02:33.050","Text":"Meaning it has its own either affinity or less ability to form an Alpha helix."},{"Start":"02:33.050 ","End":"02:35.075","Text":"We mentioned alanine, A,"},{"Start":"02:35.075 ","End":"02:37.730","Text":"as showing the greatest tendency to form alpha helices."},{"Start":"02:37.730 ","End":"02:44.520","Text":"If you just get a chain of alanines 1 after the other,"},{"Start":"02:45.310 ","End":"02:50.790","Text":"A-A-A, they will naturally form an Alpha helix."}],"ID":29580},{"Watched":false,"Name":"Exercise 7","Duration":"4m 6s","ChapterTopicVideoID":28356,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.645","Text":"Let\u0027s go with another question about secondary structure of proteins."},{"Start":"00:03.645 ","End":"00:06.450","Text":"Complete the statements by filling out the blanks."},{"Start":"00:06.450 ","End":"00:12.135","Text":"In 1951, Pauling and Corey predicted a blank type of repetitive structure,"},{"Start":"00:12.135 ","End":"00:17.360","Text":"the blank which is a more extended conformation of polypeptide chains."},{"Start":"00:17.360 ","End":"00:20.715","Text":"Going to the next part, the backbone of the polypeptide in this arrangement is"},{"Start":"00:20.715 ","End":"00:25.185","Text":"extended into a blank rather than helical structure."},{"Start":"00:25.185 ","End":"00:29.161","Text":"The arrangement of several such blank segments side by side,"},{"Start":"00:29.161 ","End":"00:34.775","Text":"all of which are in the blank is called the blank and has pleated appearance."},{"Start":"00:34.775 ","End":"00:38.315","Text":"We have a few hints as to what we\u0027re talking about."},{"Start":"00:38.315 ","End":"00:41.480","Text":"Pleated appearance, what did we talk about this?"},{"Start":"00:41.480 ","End":"00:44.870","Text":"Something that is rather than helical structure,"},{"Start":"00:44.870 ","End":"00:47.000","Text":"so it\u0027s not the helical structure,"},{"Start":"00:47.000 ","End":"00:50.150","Text":"and it\u0027s a 1951 or some later time."},{"Start":"00:50.150 ","End":"00:51.950","Text":"They did predict secondary structure,"},{"Start":"00:51.950 ","End":"00:54.485","Text":"but the first one they predicted was what?"},{"Start":"00:54.485 ","End":"00:56.270","Text":"What is what came after?"},{"Start":"00:56.270 ","End":"00:57.440","Text":"This is not the first one."},{"Start":"00:57.440 ","End":"01:01.175","Text":"It is something of a type of repetitive structure,"},{"Start":"01:01.175 ","End":"01:06.695","Text":"and it is a more extended conformation of polypeptide chains."},{"Start":"01:06.695 ","End":"01:13.700","Text":"With these hints, hopefully you got this right, but 1951,"},{"Start":"01:13.700 ","End":"01:18.380","Text":"Pauling and Corey predicted a second type of"},{"Start":"01:18.380 ","End":"01:21.830","Text":"repetitive structure because the first one they predicted"},{"Start":"01:21.830 ","End":"01:25.310","Text":"earlier on was the Alpha helix,"},{"Start":"01:25.310 ","End":"01:30.320","Text":"and they actually cite and turned it to Alpha helix."},{"Start":"01:30.320 ","End":"01:34.820","Text":"They predicted a second type of repetitive structure,"},{"Start":"01:34.820 ","End":"01:39.904","Text":"and d, which is a more extended conformation of polypeptide chains,"},{"Start":"01:39.904 ","End":"01:42.230","Text":"what is this repetitive structure?"},{"Start":"01:42.230 ","End":"01:45.975","Text":"What is this? It is the Beta conformation."},{"Start":"01:45.975 ","End":"01:49.685","Text":"First came Alpha, then came Beta."},{"Start":"01:49.685 ","End":"01:53.225","Text":"This is A and B of the alphabet."},{"Start":"01:53.225 ","End":"01:57.875","Text":"It\u0027s not that the structures actually look like Alpha or Beta,"},{"Start":"01:57.875 ","End":"02:02.455","Text":"it\u0027s just what they discovered as in time with logical A,"},{"Start":"02:02.455 ","End":"02:04.185","Text":"B, 1, 2."},{"Start":"02:04.185 ","End":"02:07.490","Text":"The second type of repetitive structure was the Beta conformation,"},{"Start":"02:07.490 ","End":"02:10.385","Text":"which is a more extended conformation of polypeptide chains."},{"Start":"02:10.385 ","End":"02:11.900","Text":"Let\u0027s move to the next section."},{"Start":"02:11.900 ","End":"02:15.980","Text":"The backbone of the polypeptide in this arrangement is extended"},{"Start":"02:15.980 ","End":"02:20.960","Text":"into a what rather than helical structure?"},{"Start":"02:20.960 ","End":"02:23.540","Text":"What is the arrangement?"},{"Start":"02:23.540 ","End":"02:26.060","Text":"What did we mention it to have?"},{"Start":"02:26.060 ","End":"02:29.525","Text":"Well, we mentioned and drew out a zigzag."},{"Start":"02:29.525 ","End":"02:33.740","Text":"The backbone of the polypeptide and the Beta conformation is"},{"Start":"02:33.740 ","End":"02:38.555","Text":"extended into a zigzag rather than helical structure."},{"Start":"02:38.555 ","End":"02:39.995","Text":"Let\u0027s go to the next part."},{"Start":"02:39.995 ","End":"02:43.969","Text":"The arrangement of several such segments side by side."},{"Start":"02:43.969 ","End":"02:45.905","Text":"We mentioned what these are,"},{"Start":"02:45.905 ","End":"02:47.915","Text":"all of which are in the,"},{"Start":"02:47.915 ","End":"02:49.850","Text":"is called the,"},{"Start":"02:49.850 ","End":"02:52.520","Text":"and has pleated appearance."},{"Start":"02:52.520 ","End":"02:56.385","Text":"Now we need to think back a little bit,"},{"Start":"02:56.385 ","End":"02:58.175","Text":"take a step back and think,"},{"Start":"02:58.175 ","End":"02:59.555","Text":"what are we talking about?"},{"Start":"02:59.555 ","End":"03:04.865","Text":"The arrangement of several such we just mentioned. What shape."},{"Start":"03:04.865 ","End":"03:09.170","Text":"Such zigzag segments side by side,"},{"Start":"03:09.170 ","End":"03:12.755","Text":"all of which are in what conformation? We just mentioned."},{"Start":"03:12.755 ","End":"03:15.740","Text":"This here, now we can bring this here."},{"Start":"03:15.740 ","End":"03:19.955","Text":"Beta conformation is called the?"},{"Start":"03:19.955 ","End":"03:23.140","Text":"What was the term for this?"},{"Start":"03:23.140 ","End":"03:30.319","Text":"We also gave an alternative term for it being the pleated version."},{"Start":"03:30.319 ","End":"03:36.340","Text":"This is called the Beta sheet and has a pleated appearance."},{"Start":"03:36.340 ","End":"03:40.220","Text":"In 1951, Pauling and Corey predicted"},{"Start":"03:40.220 ","End":"03:44.315","Text":"a second type of repetitive structure, the Beta conformation."},{"Start":"03:44.315 ","End":"03:46.970","Text":"This is more extended conformation of"},{"Start":"03:46.970 ","End":"03:51.320","Text":"polypeptide chains with a backbone of the polypeptide in this arrangement"},{"Start":"03:51.320 ","End":"03:53.930","Text":"extending into a zigzag shape rather than"},{"Start":"03:53.930 ","End":"03:58.760","Text":"helical structure and the arrangement of several such zigzag segments side by side,"},{"Start":"03:58.760 ","End":"04:01.550","Text":"all of which are in the Beta conformation is called the"},{"Start":"04:01.550 ","End":"04:05.520","Text":"Beta sheet and has a pleated appearance."}],"ID":29581},{"Watched":false,"Name":"Exercise 8","Duration":"4m 9s","ChapterTopicVideoID":28357,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.440 ","End":"00:05.685","Text":"What else did we learn in secondary structures of proteins?"},{"Start":"00:05.685 ","End":"00:08.910","Text":"Which statement about the Beta sheet is false?"},{"Start":"00:08.910 ","End":"00:11.730","Text":"We\u0027re looking for false statement."},{"Start":"00:11.730 ","End":"00:14.310","Text":"A, hydrogen bonds are formed between"},{"Start":"00:14.310 ","End":"00:18.010","Text":"the adjacent segments of polypeptide chains in the Beta sheet."},{"Start":"00:18.010 ","End":"00:20.040","Text":"B, the individual segments that form"},{"Start":"00:20.040 ","End":"00:22.905","Text":"a Beta sheet are usually nearby on the polypeptide chain,"},{"Start":"00:22.905 ","End":"00:26.640","Text":"but can also be distant from each other in the linear sequence of the polypeptide."},{"Start":"00:26.640 ","End":"00:30.089","Text":"They may even be segments in different polypeptide chains."},{"Start":"00:30.089 ","End":"00:32.070","Text":"C, the R groups of"},{"Start":"00:32.070 ","End":"00:35.760","Text":"adjacent amino acids protrude from the zigzag structure in opposite directions,"},{"Start":"00:35.760 ","End":"00:38.250","Text":"creating an alternating pattern."},{"Start":"00:38.250 ","End":"00:43.840","Text":"D, the adjacent polypeptide chains in a Beta sheet are parallel to each other."},{"Start":"00:43.840 ","End":"00:48.350","Text":"E, when 2 or more Beta sheets are layered close together within a protein,"},{"Start":"00:48.350 ","End":"00:49.940","Text":"the R groups of the amino acid residues on"},{"Start":"00:49.940 ","End":"00:52.699","Text":"the touching surfaces must be relatively small."},{"Start":"00:52.699 ","End":"00:54.855","Text":"F, none of the above."},{"Start":"00:54.855 ","End":"00:56.675","Text":"We\u0027re looking for false statement."},{"Start":"00:56.675 ","End":"00:58.760","Text":"Let\u0027s go over A again."},{"Start":"00:58.760 ","End":"01:00.560","Text":"Hydrogen bonds are formed between"},{"Start":"01:00.560 ","End":"01:04.295","Text":"the adjacent segments of polypeptide chains in the Beta sheet."},{"Start":"01:04.295 ","End":"01:05.945","Text":"Yes, this is true."},{"Start":"01:05.945 ","End":"01:10.730","Text":"We mentioned hydrogen bonds in Alpha helices as stabilizing the helix structure."},{"Start":"01:10.730 ","End":"01:13.730","Text":"We also mentioned hydrogen bonds as"},{"Start":"01:13.730 ","End":"01:17.780","Text":"forming between the adjacent segments of the polypeptide chains,"},{"Start":"01:17.780 ","End":"01:22.595","Text":"and this is how the Beta sheet is formed from the Beta conformations."},{"Start":"01:22.595 ","End":"01:24.110","Text":"This is a true statement,"},{"Start":"01:24.110 ","End":"01:26.435","Text":"therefore, it is not our answer."},{"Start":"01:26.435 ","End":"01:29.180","Text":"B, the individual segments that form"},{"Start":"01:29.180 ","End":"01:32.030","Text":"a Beta sheet are usually nearby on the polypeptide chain,"},{"Start":"01:32.030 ","End":"01:36.530","Text":"but can also be distant from each other in the linear sequence of the polypeptide,"},{"Start":"01:36.530 ","End":"01:40.135","Text":"and they may even be segments in different polypeptide chains."},{"Start":"01:40.135 ","End":"01:41.675","Text":"This most definitely is true."},{"Start":"01:41.675 ","End":"01:45.710","Text":"We literally said this verbatim in the lesson,"},{"Start":"01:45.710 ","End":"01:47.900","Text":"therefore, this is not our answer."},{"Start":"01:47.900 ","End":"01:51.995","Text":"C, the R groups of adjacent amino acids,"},{"Start":"01:51.995 ","End":"01:55.070","Text":"they protrude from the zigzag structure in opposite directions,"},{"Start":"01:55.070 ","End":"01:57.605","Text":"creating an alternating pattern."},{"Start":"01:57.605 ","End":"02:01.370","Text":"We also mentioned that the R groups do protrude in"},{"Start":"02:01.370 ","End":"02:06.260","Text":"opposite directions in the adjacent amino acids,"},{"Start":"02:06.260 ","End":"02:09.995","Text":"and therefore the statement is true and is not our answer."},{"Start":"02:09.995 ","End":"02:15.470","Text":"D, the adjacent polypeptide chains in a Beta sheet are parallel to each other."},{"Start":"02:15.470 ","End":"02:21.745","Text":"We talked about there being parallel and anti-parallel sheets."},{"Start":"02:21.745 ","End":"02:24.230","Text":"This one is questionable."},{"Start":"02:24.230 ","End":"02:27.965","Text":"It may be that the statement is not precise,"},{"Start":"02:27.965 ","End":"02:32.360","Text":"therefore, we will move on to the next ones before we eliminate this one."},{"Start":"02:32.360 ","End":"02:38.615","Text":"Let\u0027s go to E. When 2 or more Beta sheets are layered close together within a protein,"},{"Start":"02:38.615 ","End":"02:40.670","Text":"the R groups of the amino acid residues on"},{"Start":"02:40.670 ","End":"02:42.800","Text":"the touching surfaces must be relatively small."},{"Start":"02:42.800 ","End":"02:45.980","Text":"Well, here we talked about the amino acid sequences and"},{"Start":"02:45.980 ","End":"02:48.320","Text":"actual residues as part of the structure that this"},{"Start":"02:48.320 ","End":"02:51.170","Text":"can affect the formation of the structure,"},{"Start":"02:51.170 ","End":"02:53.940","Text":"so yes, for a Beta sheet to"},{"Start":"02:53.940 ","End":"02:57.619","Text":"have 2 or more where they\u0027re close together within a protein,"},{"Start":"02:57.619 ","End":"03:01.460","Text":"the amino acid residues on the touching surfaces must be relatively small."},{"Start":"03:01.460 ","End":"03:06.335","Text":"If they\u0027re bulky, then it doesn\u0027t arrange closely together within a protein."},{"Start":"03:06.335 ","End":"03:12.169","Text":"This seems like it is a true statement and therefore it\u0027s not our statement."},{"Start":"03:12.169 ","End":"03:14.315","Text":"We can eliminate this one as well."},{"Start":"03:14.315 ","End":"03:17.375","Text":"Now it leaves us with either none of the above,"},{"Start":"03:17.375 ","End":"03:20.905","Text":"if D is true or if D is false,"},{"Start":"03:20.905 ","End":"03:22.879","Text":"D is our statement."},{"Start":"03:22.879 ","End":"03:25.325","Text":"Well, going back to this,"},{"Start":"03:25.325 ","End":"03:29.615","Text":"the adjacent polypeptide chains in a Beta sheet are parallel to each other."},{"Start":"03:29.615 ","End":"03:33.405","Text":"When you have polypeptide chains that"},{"Start":"03:33.405 ","End":"03:38.275","Text":"are in a Beta conformation and arranged to form the Beta sheet,"},{"Start":"03:38.275 ","End":"03:45.440","Text":"they can form either in a parallel or anti-parallel arrangement."},{"Start":"03:45.440 ","End":"03:48.290","Text":"Therefore, this seems like it\u0027s false,"},{"Start":"03:48.290 ","End":"03:54.780","Text":"which means we can eliminate F and it leaves us with D as the false statement."},{"Start":"03:54.780 ","End":"03:57.155","Text":"How can we correct this statement?"},{"Start":"03:57.155 ","End":"03:59.535","Text":"The false statement is the adjacent polypeptide chains"},{"Start":"03:59.535 ","End":"04:01.460","Text":"and a Beta sheet are parallel to each other,"},{"Start":"04:01.460 ","End":"04:04.790","Text":"but what would make it correct is if we\u0027d say the adjacent polypeptide chains in"},{"Start":"04:04.790 ","End":"04:09.270","Text":"a Beta sheet can be either parallel or anti-parallel."}],"ID":29582},{"Watched":false,"Name":"Exercise 9","Duration":"43s","ChapterTopicVideoID":28358,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.930","Text":"You have another exercise within protein structure,"},{"Start":"00:03.930 ","End":"00:06.300","Text":"talking about secondary structures of proteins."},{"Start":"00:06.300 ","End":"00:08.010","Text":"What is an additional common type of"},{"Start":"00:08.010 ","End":"00:12.090","Text":"Beta conformation other than the Beta sheet and describe this?"},{"Start":"00:12.090 ","End":"00:18.585","Text":"We closed up the lesson talking about Beta turns and these are common in proteins."},{"Start":"00:18.585 ","End":"00:21.120","Text":"These are the connecting elements that link"},{"Start":"00:21.120 ","End":"00:24.105","Text":"successive rounds of Alpha helix or Beta conformation."},{"Start":"00:24.105 ","End":"00:27.360","Text":"Particularly common, are Beta turns to connect the ends of"},{"Start":"00:27.360 ","End":"00:30.855","Text":"2 adjacent segments of an antiparallel Beta sheet."},{"Start":"00:30.855 ","End":"00:35.490","Text":"The structure is a 180 degree turn involving 4 amino acid residues with"},{"Start":"00:35.490 ","End":"00:38.250","Text":"the carbonyl oxygen of the first residue forming"},{"Start":"00:38.250 ","End":"00:42.850","Text":"a hydrogen bond with the amino group hydrogen of the fourth."}],"ID":29583},{"Watched":false,"Name":"Tertiary and Quaternary Structure Part 1","Duration":"6m 28s","ChapterTopicVideoID":28362,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.410","Text":"We\u0027ve learned about protein structure and we are now going"},{"Start":"00:04.410 ","End":"00:08.700","Text":"to go into details about tertiary and quaternary structure."},{"Start":"00:08.700 ","End":"00:11.580","Text":"By the end of this section, you should be able to fully"},{"Start":"00:11.580 ","End":"00:17.550","Text":"understand the complexities of these levels of protein structure."},{"Start":"00:17.550 ","End":"00:21.190","Text":"We\u0027re going to split this lesson into 2 parts."},{"Start":"00:21.190 ","End":"00:23.850","Text":"The overall 3-dimensional arrangement of all atoms"},{"Start":"00:23.850 ","End":"00:26.415","Text":"in a protein is the protein\u0027s tertiary structure."},{"Start":"00:26.415 ","End":"00:30.750","Text":"Whereas the term secondary structure refers to the spatial arrangement"},{"Start":"00:30.750 ","End":"00:35.445","Text":"of amino acid residues that are adjacent in the primary structure."},{"Start":"00:35.445 ","End":"00:41.640","Text":"Tertiary structure includes longer range aspects of amino acid sequence."},{"Start":"00:41.640 ","End":"00:45.050","Text":"We talked about primary, secondary, and tertiary,"},{"Start":"00:45.050 ","End":"00:49.115","Text":"and now we\u0027re diving in specifically to tertiary structure."},{"Start":"00:49.115 ","End":"00:51.170","Text":"Amino acids that are far apart in"},{"Start":"00:51.170 ","End":"00:53.960","Text":"the polypeptide sequence and that reside in different types of"},{"Start":"00:53.960 ","End":"00:55.760","Text":"secondary structure may interact within"},{"Start":"00:55.760 ","End":"00:59.300","Text":"the completely folded structure of a protein, as you see here."},{"Start":"00:59.300 ","End":"01:00.740","Text":"As it fold,"},{"Start":"01:00.740 ","End":"01:05.015","Text":"they can interact and form disulfide bonds or hydrogen bonding."},{"Start":"01:05.015 ","End":"01:08.435","Text":"The location of bends,"},{"Start":"01:08.435 ","End":"01:09.935","Text":"including Beta turns,"},{"Start":"01:09.935 ","End":"01:11.790","Text":"in the polypeptide chain,"},{"Start":"01:11.790 ","End":"01:16.130","Text":"and the direction and angle of these bends are"},{"Start":"01:16.130 ","End":"01:21.080","Text":"determined by the number and location of specific bend-producing residues,"},{"Start":"01:21.080 ","End":"01:24.625","Text":"such as proline, threonine, serine, and glycine."},{"Start":"01:24.625 ","End":"01:28.505","Text":"Interacting segments of polypeptide chains"},{"Start":"01:28.505 ","End":"01:32.330","Text":"are held in their characteristic tertiary positions by"},{"Start":"01:32.330 ","End":"01:36.920","Text":"several weak bonding interactions and sometimes"},{"Start":"01:36.920 ","End":"01:41.945","Text":"by covalent bonds such as disulfide cross-links between the segments."},{"Start":"01:41.945 ","End":"01:45.920","Text":"Some proteins contain 2 or more separate polypeptide chains or"},{"Start":"01:45.920 ","End":"01:50.310","Text":"subunits which may be identical or different."},{"Start":"01:50.310 ","End":"01:55.560","Text":"You see here, you have this subunit and you see it marked here,"},{"Start":"01:55.560 ","End":"01:58.440","Text":"and you see there\u0027s a second one identical."},{"Start":"01:58.440 ","End":"02:04.585","Text":"So there\u0027s 2 of these that come together and assemble together into this structure."},{"Start":"02:04.585 ","End":"02:08.100","Text":"The arrangement of these protein subunits in"},{"Start":"02:08.100 ","End":"02:13.250","Text":"3-dimensional complexes constitutes the quaternary structure."},{"Start":"02:13.250 ","End":"02:15.965","Text":"We\u0027re going to talk about this in further detail."},{"Start":"02:15.965 ","End":"02:20.000","Text":"Here you see another illustration and aggregation of 2 or more polypeptides."},{"Start":"02:20.000 ","End":"02:21.335","Text":"You see 4 here."},{"Start":"02:21.335 ","End":"02:27.635","Text":"It seems like there are 2 identical of these and 2 identical of these,"},{"Start":"02:27.635 ","End":"02:30.785","Text":"and it comes together in this quaternary structure."},{"Start":"02:30.785 ","End":"02:32.480","Text":"Here there\u0027s 4 sub-units,"},{"Start":"02:32.480 ","End":"02:36.670","Text":"it\u0027s made up of 2 sets of 2 identical subunits."},{"Start":"02:36.670 ","End":"02:39.140","Text":"Here it\u0027s possibly the same idea,"},{"Start":"02:39.140 ","End":"02:42.425","Text":"2 identical subunits and 2 identical subunits."},{"Start":"02:42.425 ","End":"02:45.470","Text":"The quaternary structure of a protein is the association of"},{"Start":"02:45.470 ","End":"02:50.075","Text":"several protein chains or subunits into a closely packed arrangement."},{"Start":"02:50.075 ","End":"02:54.295","Text":"Again, as you see illustrated in these figures."},{"Start":"02:54.295 ","End":"02:57.034","Text":"Each of the subunits has its own primary,"},{"Start":"02:57.034 ","End":"02:59.405","Text":"secondary, and tertiary structure."},{"Start":"02:59.405 ","End":"03:01.130","Text":"If we\u0027re looking here, this is"},{"Start":"03:01.130 ","End":"03:05.510","Text":"a tertiary structure and you\u0027re seeing there is the secondary structure,"},{"Start":"03:05.510 ","End":"03:08.645","Text":"this Alpha helix that\u0027s portrayed here, and it\u0027s made up."},{"Start":"03:08.645 ","End":"03:10.400","Text":"You see these individual colors?"},{"Start":"03:10.400 ","End":"03:15.365","Text":"These are the amino acid residues that represent the actual primary structure,"},{"Start":"03:15.365 ","End":"03:17.495","Text":"the amino acid sequence."},{"Start":"03:17.495 ","End":"03:23.210","Text":"So each of the subunits has its own primary, secondary,"},{"Start":"03:23.210 ","End":"03:26.030","Text":"and tertiary structure that build up to make"},{"Start":"03:26.030 ","End":"03:29.495","Text":"the quaternary structure, the assembled subunits."},{"Start":"03:29.495 ","End":"03:33.770","Text":"You\u0027re seeing different illustrations of the same concepts."},{"Start":"03:33.770 ","End":"03:36.560","Text":"The subunits are held together by hydrogen bonds and"},{"Start":"03:36.560 ","End":"03:39.920","Text":"van der Waals forces between non-polar side chains."},{"Start":"03:39.920 ","End":"03:44.210","Text":"A protein quaternary structure is the number and arrangement of multiple"},{"Start":"03:44.210 ","End":"03:49.100","Text":"folded protein subunits in a multicellular complex and"},{"Start":"03:49.100 ","End":"03:52.190","Text":"includes organizations from simple dimers to"},{"Start":"03:52.190 ","End":"03:59.380","Text":"large homo-oligomers and complexes with defined or variable numbers of units."},{"Start":"03:59.380 ","End":"04:01.430","Text":"Here\u0027s a different figure,"},{"Start":"04:01.430 ","End":"04:02.960","Text":"that we haven\u0027t seen this far,"},{"Start":"04:02.960 ","End":"04:04.380","Text":"portraying the same idea."},{"Start":"04:04.380 ","End":"04:07.340","Text":"You have a linear sequence of amino acids."},{"Start":"04:07.340 ","End":"04:09.290","Text":"This is the primary sequence."},{"Start":"04:09.290 ","End":"04:15.380","Text":"You have the secondary sequence which is made up of either Alpha helices,"},{"Start":"04:15.380 ","End":"04:17.780","Text":"which are the most common, and Beta sheets,"},{"Start":"04:17.780 ","End":"04:19.445","Text":"which are again common."},{"Start":"04:19.445 ","End":"04:20.855","Text":"You also have Beta turns."},{"Start":"04:20.855 ","End":"04:23.140","Text":"These are the 2 most common."},{"Start":"04:23.140 ","End":"04:26.780","Text":"These come together to form the tertiary sequence,"},{"Start":"04:26.780 ","End":"04:28.190","Text":"which is a polypeptide chain with"},{"Start":"04:28.190 ","End":"04:33.170","Text":"protein secondary structures that interact with each other and fold upon itself."},{"Start":"04:33.170 ","End":"04:37.505","Text":"Here you see an Alpha helix and here you see Beta sheets."},{"Start":"04:37.505 ","End":"04:40.040","Text":"These come together when you have multiple of these,"},{"Start":"04:40.040 ","End":"04:41.860","Text":"multiple protein subunit,"},{"Start":"04:41.860 ","End":"04:43.990","Text":"in 1 complex as the quaternary structure."},{"Start":"04:43.990 ","End":"04:46.105","Text":"You see multiples of this."},{"Start":"04:46.105 ","End":"04:49.663","Text":"You see 1, 2, 3, 4,"},{"Start":"04:49.663 ","End":"04:52.250","Text":"5 of these subunits coming together in"},{"Start":"04:52.250 ","End":"04:56.630","Text":"this quaternary structure where you have these Alpha helixes in the center,"},{"Start":"04:56.630 ","End":"04:59.385","Text":"and you have the Beta sheets coming together."},{"Start":"04:59.385 ","End":"05:02.030","Text":"Considering these higher levels of structure,"},{"Start":"05:02.030 ","End":"05:07.850","Text":"it is useful to designate 2 major groups into which many proteins can be classified."},{"Start":"05:07.850 ","End":"05:14.300","Text":"There\u0027s fibrous proteins having polypeptide chains arranged in long strands or sheets."},{"Start":"05:14.300 ","End":"05:19.265","Text":"This is an example of fibrous protein and it\u0027s a long strand."},{"Start":"05:19.265 ","End":"05:22.400","Text":"You have globular proteins having"},{"Start":"05:22.400 ","End":"05:26.135","Text":"polypeptide chains folded into spherical or globular shape."},{"Start":"05:26.135 ","End":"05:29.030","Text":"This is the globular protein."},{"Start":"05:29.030 ","End":"05:30.634","Text":"It\u0027s more of a bundle."},{"Start":"05:30.634 ","End":"05:33.365","Text":"These 2 groups are structurally distinct."},{"Start":"05:33.365 ","End":"05:38.719","Text":"Fibrous proteins usually consists largely of a single type of secondary structure."},{"Start":"05:38.719 ","End":"05:43.515","Text":"You see here, it\u0027s a helical structure, intertwined."},{"Start":"05:43.515 ","End":"05:48.680","Text":"While globular proteins often contain several types of secondary structure."},{"Start":"05:48.680 ","End":"05:55.900","Text":"What you see here is another ribbon illustration of the globular protein."},{"Start":"05:55.900 ","End":"06:01.175","Text":"The 2 groups differ functionally in that the structures that provide support, shape,"},{"Start":"06:01.175 ","End":"06:05.030","Text":"and external protection to vertebrates are made of fibrous proteins,"},{"Start":"06:05.030 ","End":"06:09.055","Text":"whereas most enzymes and regulatory proteins are globular proteins."},{"Start":"06:09.055 ","End":"06:13.550","Text":"Certain fibers proteins play a key role in the development of our modern understanding of"},{"Start":"06:13.550 ","End":"06:14.750","Text":"protein structure and provide"},{"Start":"06:14.750 ","End":"06:18.830","Text":"particularly clear examples of the relationship between structure and function."},{"Start":"06:18.830 ","End":"06:21.950","Text":"With this, we conclude Part I of tertiary and quaternary structure."},{"Start":"06:21.950 ","End":"06:28.020","Text":"You should have a better understanding of tertiary and quaternary structure of proteins."}],"ID":29584},{"Watched":false,"Name":"Tertiary and Quaternary Structure Part 2","Duration":"8m 4s","ChapterTopicVideoID":28363,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.130","Text":"We are continuing our lesson on tertiary and quaternary structure, Part 2."},{"Start":"00:05.130 ","End":"00:10.020","Text":"Protein quaternary structures range from simple dimers to large complexes."},{"Start":"00:10.020 ","End":"00:13.050","Text":"Many proteins have multiple polypeptide subunits."},{"Start":"00:13.050 ","End":"00:17.880","Text":"The association of polypeptide chains can serve a variety of functions."},{"Start":"00:17.880 ","End":"00:21.825","Text":"Many multisubunit proteins have regulatory roles."},{"Start":"00:21.825 ","End":"00:26.850","Text":"The binding of small molecules may affect the interaction between subunits causing"},{"Start":"00:26.850 ","End":"00:29.490","Text":"large changes in the protein\u0027s activity in response to"},{"Start":"00:29.490 ","End":"00:33.390","Text":"small changes in the concentration of substrate or regulatory molecules."},{"Start":"00:33.390 ","End":"00:38.630","Text":"In some cases, separate subunits can take on separate but related functions,"},{"Start":"00:38.630 ","End":"00:41.285","Text":"such as catalysis and regulation."},{"Start":"00:41.285 ","End":"00:44.270","Text":"Some associations, such as the fibrous proteins"},{"Start":"00:44.270 ","End":"00:47.525","Text":"mentioned earlier in the chapter and the co-proteins of viruses,"},{"Start":"00:47.525 ","End":"00:50.540","Text":"serve primarily structural roles."},{"Start":"00:50.540 ","End":"00:56.200","Text":"Some very large protein assemblies are the site of complex multistep reactions."},{"Start":"00:56.200 ","End":"00:59.750","Text":"One example of this is the ribosome."},{"Start":"00:59.750 ","End":"01:04.070","Text":"It\u0027s the site of protein synthesis which incorporates dozens of"},{"Start":"01:04.070 ","End":"01:08.947","Text":"proteins subunits along with a number of RNA molecules,"},{"Start":"01:08.947 ","End":"01:10.450","Text":"so you have the ribosome,"},{"Start":"01:10.450 ","End":"01:14.635","Text":"you have the 2 major RNA subunits,"},{"Start":"01:14.635 ","End":"01:21.160","Text":"and you have its association of the different RNAs that come into it."},{"Start":"01:21.160 ","End":"01:22.610","Text":"If you come and look here,"},{"Start":"01:22.610 ","End":"01:24.260","Text":"prokaryotic and eukaryotic again,"},{"Start":"01:24.260 ","End":"01:25.570","Text":"you have the ribosome."},{"Start":"01:25.570 ","End":"01:27.215","Text":"It\u0027s a little different."},{"Start":"01:27.215 ","End":"01:28.760","Text":"While same idea,"},{"Start":"01:28.760 ","End":"01:37.763","Text":"2 major subunits made up of 2 RNA subunits,"},{"Start":"01:37.763 ","End":"01:43.804","Text":"and you have these RNAs that associate with proteins and make this complex."},{"Start":"01:43.804 ","End":"01:48.550","Text":"Again, you see here RNAs that associate with proteins and make this complex."},{"Start":"01:48.550 ","End":"01:52.625","Text":"A multisubunit protein is also referred to as a multimer."},{"Start":"01:52.625 ","End":"01:58.000","Text":"Multimeric proteins can have from 2-100s of subunits."},{"Start":"01:58.000 ","End":"02:02.685","Text":"A multimer with just a few subunits is often called an oligomer."},{"Start":"02:02.685 ","End":"02:05.540","Text":"Hemoglobin, which we mentioned previously,"},{"Start":"02:05.540 ","End":"02:08.160","Text":"for example, is one of these."},{"Start":"02:08.160 ","End":"02:11.974","Text":"Hemoglobin, which we had mentioned just previously,"},{"Start":"02:11.974 ","End":"02:14.305","Text":"is an example of such."},{"Start":"02:14.305 ","End":"02:18.740","Text":"If a multimer is composed of a number of non-identical subunits,"},{"Start":"02:18.740 ","End":"02:23.960","Text":"the overall structure of the protein can be asymmetric and quite complicated."},{"Start":"02:23.960 ","End":"02:26.660","Text":"However, most multimers have"},{"Start":"02:26.660 ","End":"02:30.335","Text":"identical subunits or repeating groups of non-identical subunits,"},{"Start":"02:30.335 ","End":"02:33.880","Text":"usually in symmetric arrangements."},{"Start":"02:33.880 ","End":"02:36.125","Text":"As I mentioned in an earlier lesson,"},{"Start":"02:36.125 ","End":"02:40.910","Text":"the repeating structural unit in a multimeric protein is called a protomer,"},{"Start":"02:40.910 ","End":"02:45.070","Text":"whether it is a single subunit or a group of subunits."},{"Start":"02:45.070 ","End":"02:47.370","Text":"The first oligomeric protein for which"},{"Start":"02:47.370 ","End":"02:51.035","Text":"the 3-dimensional structure was determined was hemoglobin,"},{"Start":"02:51.035 ","End":"02:53.765","Text":"which contains 4 polypeptide chains,"},{"Start":"02:53.765 ","End":"02:55.060","Text":"as seen here,"},{"Start":"02:55.060 ","End":"03:02.825","Text":"and this is 1 subunit and 4 heme prosthetic groups as seen here."},{"Start":"03:02.825 ","End":"03:05.540","Text":"This is one. Again here,"},{"Start":"03:05.540 ","End":"03:10.005","Text":"this is 1 heme 2, 3, 4."},{"Start":"03:10.005 ","End":"03:12.375","Text":"In this 4 heme prosthetic groups,"},{"Start":"03:12.375 ","End":"03:16.275","Text":"iron atoms are in the ferrous Fe_2 state."},{"Start":"03:16.275 ","End":"03:20.800","Text":"The protein portion called globin consists of 2 chains,"},{"Start":"03:20.800 ","End":"03:23.625","Text":"each of 141 residues,"},{"Start":"03:23.625 ","End":"03:29.165","Text":"and 2 additional chains of 146 residues each."},{"Start":"03:29.165 ","End":"03:32.555","Text":"The subunits of hemoglobin are arranged in symmetric pairs,"},{"Start":"03:32.555 ","End":"03:37.100","Text":"each pair having 1 Alpha and 1 Beta subunit."},{"Start":"03:37.100 ","End":"03:39.970","Text":"As you see here, there\u0027s an Alpha subunit,"},{"Start":"03:39.970 ","End":"03:44.723","Text":"another Alpha, and a Beta subunit and another Beta subunit,"},{"Start":"03:44.723 ","End":"03:46.565","Text":"so you have symmetric pairs,"},{"Start":"03:46.565 ","End":"03:50.345","Text":"each having 1 pair of Alpha subunits,"},{"Start":"03:50.345 ","End":"03:52.615","Text":"1 pair of Beta subunits."},{"Start":"03:52.615 ","End":"03:55.250","Text":"This is just another illustration and again,"},{"Start":"03:55.250 ","End":"03:58.465","Text":"you have the 4 hemes right here."},{"Start":"03:58.465 ","End":"04:03.605","Text":"Hemoglobin can therefore be described either as a tetramer,"},{"Start":"04:03.605 ","End":"04:07.595","Text":"meaning 4, remember this word tetra,"},{"Start":"04:07.595 ","End":"04:10.220","Text":"or as a dimer."},{"Start":"04:10.220 ","End":"04:12.805","Text":"Then here you would have 1,"},{"Start":"04:12.805 ","End":"04:14.295","Text":"2, 3,"},{"Start":"04:14.295 ","End":"04:20.150","Text":"4 for the tetramer or as a dimer of Alpha-Beta protomers,"},{"Start":"04:20.150 ","End":"04:21.440","Text":"so a dimer of,"},{"Start":"04:21.440 ","End":"04:25.820","Text":"let\u0027s say Alpha and Beta, so this would be,"},{"Start":"04:25.820 ","End":"04:33.930","Text":"let\u0027s say Beta and this would be Alpha or here you have Alpha and here you have Beta."},{"Start":"04:33.930 ","End":"04:37.310","Text":"Identical subunits of multimeric proteins are"},{"Start":"04:37.310 ","End":"04:41.165","Text":"generally arranged in 1 or a limited set of symmetric patterns."},{"Start":"04:41.165 ","End":"04:46.370","Text":"Oligomers can have either rotational symmetry or helical symmetry."},{"Start":"04:46.370 ","End":"04:51.305","Text":"That is, individual subunits of these oligomers can be superimposed on"},{"Start":"04:51.305 ","End":"04:57.265","Text":"others by rotation about 1 or more rotational axis or by a helical rotation."},{"Start":"04:57.265 ","End":"04:59.180","Text":"Proteins, with rotational symmetry,"},{"Start":"04:59.180 ","End":"05:03.590","Text":"the subunits pack that the rotational axis to form closed structures."},{"Start":"05:03.590 ","End":"05:07.145","Text":"Proteins with helical symmetry tend to form structures that are more"},{"Start":"05:07.145 ","End":"05:10.985","Text":"open-ended with subunits added in a spiraling array."},{"Start":"05:10.985 ","End":"05:13.595","Text":"There are several forms of rotational symmetry,"},{"Start":"05:13.595 ","End":"05:20.510","Text":"with cyclic symmetry being the simplest one involving rotation about a single axis."},{"Start":"05:20.510 ","End":"05:24.575","Text":"A somewhat more complicated rotational symmetry is"},{"Start":"05:24.575 ","End":"05:29.735","Text":"a 2-fold rotational axis is dihedral symmetry,"},{"Start":"05:29.735 ","End":"05:36.904","Text":"in which a 2-fold rotational axis intersects an n-fold axis at right angles."},{"Start":"05:36.904 ","End":"05:40.180","Text":"This is called dihedral."},{"Start":"05:40.180 ","End":"05:44.805","Text":"The symmetry is defined as Dn."},{"Start":"05:44.805 ","End":"05:48.195","Text":"A protein with dihedral symmetry has"},{"Start":"05:48.195 ","End":"05:55.580","Text":"2n protomers because they are actually 2-fold rotations of the oligomer."},{"Start":"05:55.580 ","End":"05:59.825","Text":"Proteins with cyclic or dihedral symmetry are particularly common."},{"Start":"05:59.825 ","End":"06:02.510","Text":"More complex rotational symmetries are possible,"},{"Start":"06:02.510 ","End":"06:04.760","Text":"but only a few are regularly encountered."},{"Start":"06:04.760 ","End":"06:07.510","Text":"One example is icosahedral symmetry."},{"Start":"06:07.510 ","End":"06:12.155","Text":"The term icosahedral, it stands for an icosahedron,"},{"Start":"06:12.155 ","End":"06:17.450","Text":"which is a regular 12-cornered polyhedron having 20 equilateral triangular faces."},{"Start":"06:17.450 ","End":"06:19.385","Text":"I know that sounds heavy,"},{"Start":"06:19.385 ","End":"06:23.329","Text":"but it just means that there\u0027s 20 of these equilateral triangles."},{"Start":"06:23.329 ","End":"06:24.635","Text":"This is 1, 2,"},{"Start":"06:24.635 ","End":"06:27.585","Text":"3, 4, 5, etc."},{"Start":"06:27.585 ","End":"06:30.240","Text":"This is a common structure in virus coats,"},{"Start":"06:30.240 ","End":"06:32.810","Text":"or capsids as you can see here."},{"Start":"06:32.810 ","End":"06:36.230","Text":"This is what it would look like in a virus capsid."},{"Start":"06:36.230 ","End":"06:42.065","Text":"Poliovirus also is an example of such a virus that has an icosahedral shape."},{"Start":"06:42.065 ","End":"06:47.660","Text":"The other major type of symmetry found in oligomers is helical symmetry."},{"Start":"06:47.660 ","End":"06:49.700","Text":"This also occurs in capsids."},{"Start":"06:49.700 ","End":"06:51.995","Text":"Tobacco mosaic virus,"},{"Start":"06:51.995 ","End":"06:56.430","Text":"TMV, this was hepatitis A virus."},{"Start":"06:56.430 ","End":"06:59.600","Text":"There\u0027s also HPV and HCV."},{"Start":"06:59.600 ","End":"07:01.340","Text":"The tobacco mosaic virus is"},{"Start":"07:01.340 ","End":"07:09.490","Text":"a right-handed helical filament made up of 2,130 identical subunits."},{"Start":"07:09.490 ","End":"07:13.535","Text":"The RNA, the genetic materials inside this cylindrical structure,"},{"Start":"07:13.535 ","End":"07:15.919","Text":"encloses the viral RNA."},{"Start":"07:15.919 ","End":"07:21.620","Text":"Proteins with subunits arranged in helical filaments also occurs in capsid,"},{"Start":"07:21.620 ","End":"07:24.620","Text":"like in the case of tobacco mosaic virus."},{"Start":"07:24.620 ","End":"07:26.240","Text":"Tobacco mosaic virus is"},{"Start":"07:26.240 ","End":"07:31.490","Text":"a right-handed helical filament made up of 2,130 identical subunits."},{"Start":"07:31.490 ","End":"07:35.840","Text":"This cylindrical structure encloses the viral RNA,"},{"Start":"07:35.840 ","End":"07:38.020","Text":"the viral genetic material."},{"Start":"07:38.020 ","End":"07:39.860","Text":"Proteins with subunits arranged in"},{"Start":"07:39.860 ","End":"07:42.830","Text":"helical filaments can also form long fibrous structures,"},{"Start":"07:42.830 ","End":"07:45.410","Text":"such as the actin filaments of muscle."},{"Start":"07:45.410 ","End":"07:48.755","Text":"What you see here is an example,"},{"Start":"07:48.755 ","End":"07:55.610","Text":"an illustration of the actin helical filaments that form the actin subunit."},{"Start":"07:55.610 ","End":"08:00.698","Text":"With that, we completed the lesson on tertiary and quaternary structure,"},{"Start":"08:00.698 ","End":"08:04.620","Text":"and by now you should understand these more in depth."}],"ID":29585},{"Watched":false,"Name":"Exercise 10","Duration":"1m 14s","ChapterTopicVideoID":28359,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.420","Text":"Now that we\u0027ve learnt more in depth about tertiary and quaternary structures,"},{"Start":"00:03.420 ","End":"00:05.220","Text":"let\u0027s cover some exercises."},{"Start":"00:05.220 ","End":"00:08.220","Text":"What is protein tertiary and quaternary structure?"},{"Start":"00:08.220 ","End":"00:11.100","Text":"The overall 3-dimensional arrangement of all atoms in a protein"},{"Start":"00:11.100 ","End":"00:14.010","Text":"is referred to as a protein\u0027s tertiary structure,"},{"Start":"00:14.010 ","End":"00:17.220","Text":"whereas the term secondary structure also refers"},{"Start":"00:17.220 ","End":"00:24.420","Text":"to the special arrangement"},{"Start":"00:24.420 ","End":"00:28.020","Text":"of amino acids residues that are adjacent in the primary structure."},{"Start":"00:28.020 ","End":"00:32.475","Text":"Tertiary structure includes longer-range aspects of amino acid sequence,"},{"Start":"00:32.475 ","End":"00:35.250","Text":"where different separate segments interact with each other"},{"Start":"00:35.250 ","End":"00:37.980","Text":"and are held together in a characteristic tertiary position."},{"Start":"00:37.980 ","End":"00:37.981","Text":"This happens by different kind of weak bonding interactions and sometimes by"},{"Start":"00:37.981 ","End":"00:37.982","Text":"covalent bonds such as"},{"Start":"00:37.982 ","End":"00:37.983","Text":"disulfide bonds that happen and"},{"Start":"00:37.983 ","End":"00:38.984","Text":"crosslink between the segments."},{"Start":"00:48.410 ","End":"00:53.670","Text":"Some proteins contain 2 or more polypeptide chains"},{"Start":"00:53.670 ","End":"00:57.125","Text":"or subunits which may be identical or different."},{"Start":"00:57.125 ","End":"00:59.040","Text":"The arrangement of these protein subunits in"},{"Start":"00:59.040 ","End":"01:02.180","Text":"3-dimensional complexes constitutes quaternary structure."},{"Start":"01:02.180 ","End":"01:05.810","Text":"As you see here, this is the 1 subunit and it arranges here."},{"Start":"01:05.810 ","End":"01:09.105","Text":"There\u0027s 2 of these and it arranges with a complex"},{"Start":"01:09.105 ","End":"01:13.740","Text":"that includes 4 subunits into this quaternary structure."}],"ID":29586},{"Watched":false,"Name":"Exercise 11","Duration":"1m 21s","ChapterTopicVideoID":28360,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.755","Text":"Let\u0027s go into another exercise talking about tertiary and quaternary structure."},{"Start":"00:04.755 ","End":"00:09.465","Text":"Part I, in considering the higher levels of protein structure covered in this lesson,"},{"Start":"00:09.465 ","End":"00:12.585","Text":"it is useful to classify proteins into 2 major groups,"},{"Start":"00:12.585 ","End":"00:14.265","Text":"list these and define them."},{"Start":"00:14.265 ","End":"00:19.200","Text":"The 2 major groups proteins are classified into are fibrous proteins,"},{"Start":"00:19.200 ","End":"00:23.130","Text":"these have polypeptide chains arranged in long strands or sheets."},{"Start":"00:23.130 ","End":"00:26.010","Text":"Globular proteins, these have polypeptide chains folded"},{"Start":"00:26.010 ","End":"00:29.580","Text":"into a spherical or globular shape as seen here."},{"Start":"00:29.580 ","End":"00:34.065","Text":"Part II, explain the differences between these 2 types of protein classes."},{"Start":"00:34.065 ","End":"00:36.480","Text":"The 2 groups are structurally distinct."},{"Start":"00:36.480 ","End":"00:41.010","Text":"Fibrous proteins usually consists largely of a single type of secondary structure."},{"Start":"00:41.010 ","End":"00:46.790","Text":"As you see here it\u0027s a helical structure whereas globular proteins often contain"},{"Start":"00:46.790 ","End":"00:52.850","Text":"several types of secondary structure and are more of a compact shape."},{"Start":"00:52.850 ","End":"00:57.770","Text":"The 2 groups differ functionally in that the structures that provide"},{"Start":"00:57.770 ","End":"01:03.080","Text":"support shape and external protection to vertebrates are made of fibrous proteins,"},{"Start":"01:03.080 ","End":"01:08.750","Text":"whereas most enzyme in regulatory proteins are globular proteins."},{"Start":"01:08.750 ","End":"01:10.940","Text":"Certain fibrous proteins played"},{"Start":"01:10.940 ","End":"01:13.640","Text":"a key role in the development of our modern understanding of"},{"Start":"01:13.640 ","End":"01:16.430","Text":"protein structure and provide particularly clear examples of"},{"Start":"01:16.430 ","End":"01:20.640","Text":"the relationship between structure and function."}],"ID":29587},{"Watched":false,"Name":"Exercise 12","Duration":"3m 15s","ChapterTopicVideoID":28361,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.115","Text":"We have an additional exercise covering the lesson tertiary and quaternary structure."},{"Start":"00:05.115 ","End":"00:09.720","Text":"Which statement with regard to protein quaternary structure is false?"},{"Start":"00:09.720 ","End":"00:15.555","Text":"Protein quaternary structures range from simple dimers to large complexes. That was A."},{"Start":"00:15.555 ","End":"00:18.990","Text":"B, the quaternary structure of a protein is the association of"},{"Start":"00:18.990 ","End":"00:22.890","Text":"several protein chains or subunits into a closely packed arrangement."},{"Start":"00:22.890 ","End":"00:27.420","Text":"C, many proteins have multiple polypeptide subunits that are part of"},{"Start":"00:27.420 ","End":"00:29.760","Text":"their quaternary structure and these can take on"},{"Start":"00:29.760 ","End":"00:33.055","Text":"separate but related functions such as catalysis and regulation."},{"Start":"00:33.055 ","End":"00:36.420","Text":"D, all of the subunits of the multiple polypeptides that make up"},{"Start":"00:36.420 ","End":"00:38.430","Text":"the quaternary structure have different primary"},{"Start":"00:38.430 ","End":"00:40.920","Text":"but the same secondary and tertiary structure."},{"Start":"00:40.920 ","End":"00:44.240","Text":"E, the subunits are the multiple polypeptide are held together by"},{"Start":"00:44.240 ","End":"00:48.035","Text":"hydrogen bonds and van der Waals forces between nonpolar side chains."},{"Start":"00:48.035 ","End":"00:49.925","Text":"Let\u0027s go at this one at a time."},{"Start":"00:49.925 ","End":"00:53.210","Text":"We can eliminate statements that we know is true"},{"Start":"00:53.210 ","End":"00:56.525","Text":"because they do not complete our search for something that is false."},{"Start":"00:56.525 ","End":"00:57.950","Text":"Let\u0027s go back to A."},{"Start":"00:57.950 ","End":"01:02.795","Text":"Protein quaternary structures range from simple dimers to large complexes."},{"Start":"01:02.795 ","End":"01:05.150","Text":"Well, by the definition of quaternary structure,"},{"Start":"01:05.150 ","End":"01:10.340","Text":"it\u0027s an arrangement of multiple subunits or polypeptides,"},{"Start":"01:10.340 ","End":"01:13.190","Text":"and it can be from a simple dimer to large complex."},{"Start":"01:13.190 ","End":"01:17.210","Text":"Hence this sounds true and therefore it will not be our correct answer."},{"Start":"01:17.210 ","End":"01:21.520","Text":"We can mark this as not answer."},{"Start":"01:21.520 ","End":"01:24.980","Text":"B, the quaternary structure of a protein is the association of"},{"Start":"01:24.980 ","End":"01:28.805","Text":"several protein chains or subunits into a closely packed arrangement."},{"Start":"01:28.805 ","End":"01:30.980","Text":"Yes, that\u0027s what we just said with regard to"},{"Start":"01:30.980 ","End":"01:34.280","Text":"explaining A as being a true statement and therefore not false."},{"Start":"01:34.280 ","End":"01:36.370","Text":"So we can mark this off as well."},{"Start":"01:36.370 ","End":"01:37.880","Text":"C, many proteins have"},{"Start":"01:37.880 ","End":"01:42.115","Text":"multiple polypeptides subunits that are part of their quaternary structure,"},{"Start":"01:42.115 ","End":"01:44.960","Text":"and these can take on separate but related functions,"},{"Start":"01:44.960 ","End":"01:48.965","Text":"multiple polypeptide subunits that can take on separate but related function."},{"Start":"01:48.965 ","End":"01:50.090","Text":"We did mention this."},{"Start":"01:50.090 ","End":"01:51.530","Text":"We didn\u0027t go into this in-depth,"},{"Start":"01:51.530 ","End":"01:53.480","Text":"but this is a possibility, therefore,"},{"Start":"01:53.480 ","End":"01:55.520","Text":"this is true and not our answer."},{"Start":"01:55.520 ","End":"01:58.760","Text":"D, all of the subunits of the multiple polypeptide"},{"Start":"01:58.760 ","End":"02:02.135","Text":"that makes up the quarternary structure have different primary,"},{"Start":"02:02.135 ","End":"02:05.090","Text":"but the same secondary and tertiary structure."},{"Start":"02:05.090 ","End":"02:10.040","Text":"Well, we did not state this as part of the quaternary structure."},{"Start":"02:10.040 ","End":"02:13.880","Text":"Therefore, this sounds like it may be our correct answer,"},{"Start":"02:13.880 ","End":"02:17.300","Text":"but before we mark this let\u0027s just test E,"},{"Start":"02:17.300 ","End":"02:21.470","Text":"the subunits of the multiple polypeptide are held together by"},{"Start":"02:21.470 ","End":"02:26.195","Text":"hydrogen bonds and van der Waals forces between nonpolar side chains."},{"Start":"02:26.195 ","End":"02:32.120","Text":"We did mention this as a possibility of something that holds the subunits together."},{"Start":"02:32.120 ","End":"02:34.985","Text":"This sounds like it could be true."},{"Start":"02:34.985 ","End":"02:36.800","Text":"Therefore it\u0027s not our answer,"},{"Start":"02:36.800 ","End":"02:45.005","Text":"which then would leave us with D. D is the correct answer because it is false."},{"Start":"02:45.005 ","End":"02:47.555","Text":"How can we correct the statement?"},{"Start":"02:47.555 ","End":"02:51.620","Text":"We can correct this statement by saying each of the subunits of"},{"Start":"02:51.620 ","End":"02:56.690","Text":"a multiple polypeptide that makes up the quaternary structure has its own primary,"},{"Start":"02:56.690 ","End":"02:59.089","Text":"secondary, and tertiary structure."},{"Start":"02:59.089 ","End":"03:04.130","Text":"Now it doesn\u0027t mean that there can\u0027t be identical subunits."},{"Start":"03:04.130 ","End":"03:10.340","Text":"That can be, but it doesn\u0027t mean that all the subunits have different primary,"},{"Start":"03:10.340 ","End":"03:12.875","Text":"but the same secondary, tertiary structure."},{"Start":"03:12.875 ","End":"03:14.970","Text":"This is not true."}],"ID":29588},{"Watched":false,"Name":"Structure Classification","Duration":"5m 37s","ChapterTopicVideoID":28364,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.710","Text":"Now that we\u0027ve talked about protein structures and its complexities,"},{"Start":"00:04.710 ","End":"00:07.200","Text":"let\u0027s talk about structure classification."},{"Start":"00:07.200 ","End":"00:08.550","Text":"By the end of this section,"},{"Start":"00:08.550 ","End":"00:12.270","Text":"you\u0027ll be able to classify proteins based on structure,"},{"Start":"00:12.270 ","End":"00:16.110","Text":"and explain structure and evolutionary relationships."},{"Start":"00:16.110 ","End":"00:21.225","Text":"Protein motifs are the basis for protein structural classification."},{"Start":"00:21.225 ","End":"00:23.730","Text":"At the highest level of classification,"},{"Start":"00:23.730 ","End":"00:26.954","Text":"protein structures are divided into 4 classes."},{"Start":"00:26.954 ","End":"00:30.240","Text":"All Alpha, which means all Alpha helices."},{"Start":"00:30.240 ","End":"00:34.365","Text":"As you can see here, this is different examples of how"},{"Start":"00:34.365 ","End":"00:40.620","Text":"an all Alpha protein structure classification can be."},{"Start":"00:40.620 ","End":"00:44.160","Text":"All Beta, Beta conformations."},{"Start":"00:44.160 ","End":"00:48.370","Text":"You have the Beta conformation, the Beta sheets."},{"Start":"00:48.370 ","End":"00:53.360","Text":"Here you have a Beta barrel where it forms a barrel."},{"Start":"00:53.360 ","End":"01:00.310","Text":"Here you see additional depictions of the Beta organizations, all Beta."},{"Start":"01:00.310 ","End":"01:04.190","Text":"The third protein classification is Alpha over Beta,"},{"Start":"01:04.190 ","End":"01:08.945","Text":"in which the Alpha and Beta segments are interspersed or alternate."},{"Start":"01:08.945 ","End":"01:12.170","Text":"You see here, there\u0027s an Alpha and Beta sheets,"},{"Start":"01:12.170 ","End":"01:15.440","Text":"and another portion of Alpha or here just see Alpha and Beta"},{"Start":"01:15.440 ","End":"01:20.240","Text":"completely mixed and interspersed between themselves as well as here."},{"Start":"01:20.240 ","End":"01:22.969","Text":"This is another image showing the same idea."},{"Start":"01:22.969 ","End":"01:26.810","Text":"It\u0027s interspersed, the Alpha helices between the Beta sheets."},{"Start":"01:26.810 ","End":"01:29.540","Text":"The fourth classification is Alpha and"},{"Start":"01:29.540 ","End":"01:33.140","Text":"Beta in which the Alpha and Beta regions are somewhat segregated."},{"Start":"01:33.140 ","End":"01:35.320","Text":"You see that there\u0027s the Alpha helix here,"},{"Start":"01:35.320 ","End":"01:40.505","Text":"the Beta sheets are in a different region that you separate the same here."},{"Start":"01:40.505 ","End":"01:43.895","Text":"You have the Beta sheets here and you have an Alpha helix here,"},{"Start":"01:43.895 ","End":"01:48.200","Text":"and here you can also consider this as segregated because the Betas"},{"Start":"01:48.200 ","End":"01:53.440","Text":"are in this section and the Alpha helices are to the side."},{"Start":"01:53.440 ","End":"01:57.320","Text":"Within each class are tens to hundreds of"},{"Start":"01:57.320 ","End":"02:02.840","Text":"different folding arrangements built up from increasingly identifiable substructures."},{"Start":"02:02.840 ","End":"02:05.735","Text":"Some of the substructure arrangements are very common,"},{"Start":"02:05.735 ","End":"02:08.135","Text":"others have been found in just 1 protein."},{"Start":"02:08.135 ","End":"02:11.854","Text":"Now, generally, when you look at these ribbon diagrams,"},{"Start":"02:11.854 ","End":"02:15.725","Text":"Alpha helices are shown as these coiled ribbons,"},{"Start":"02:15.725 ","End":"02:23.615","Text":"while you can also find them as thick tubes and Beta strands tend to be shown as arrows."},{"Start":"02:23.615 ","End":"02:28.205","Text":"Non-repetitive coils or loops are lines or thin tubes."},{"Start":"02:28.205 ","End":"02:31.835","Text":"Lines are the non-repetitive coils or loops."},{"Start":"02:31.835 ","End":"02:36.500","Text":"We displayed a variety of motifs arrayed among the 4 classes of protein structure,"},{"Start":"02:36.500 ","End":"02:40.445","Text":"those illustrator just a minute sample the hundreds of known motifs."},{"Start":"02:40.445 ","End":"02:44.975","Text":"Though the number of folding patterns is not actually infinite."},{"Start":"02:44.975 ","End":"02:49.040","Text":"As the rate at which new protein structures are elucidated has increased,"},{"Start":"02:49.040 ","End":"02:53.540","Text":"the fraction of those structures containing new motif has steadily declined."},{"Start":"02:53.540 ","End":"02:57.140","Text":"Fewer than 1000 different folds or motifs exist in"},{"Start":"02:57.140 ","End":"03:00.905","Text":"all proteins as far as we know currently."},{"Start":"03:00.905 ","End":"03:03.560","Text":"The top 2 levels of organization,"},{"Start":"03:03.560 ","End":"03:06.965","Text":"class, and fold are purely structural."},{"Start":"03:06.965 ","End":"03:08.390","Text":"Below the fold level,"},{"Start":"03:08.390 ","End":"03:11.915","Text":"categorization is based on evolutionary relationships."},{"Start":"03:11.915 ","End":"03:17.010","Text":"Many examples of recurring domain or motif structures are available and these reveal"},{"Start":"03:17.010 ","End":"03:23.345","Text":"that protein tertiary structure is more reliably conserved than primary structure."},{"Start":"03:23.345 ","End":"03:29.795","Text":"The comparison of protein structures can thus provide much information about evolution."},{"Start":"03:29.795 ","End":"03:34.220","Text":"Proteins with significant primary sequence similarity and/or with"},{"Start":"03:34.220 ","End":"03:39.230","Text":"demonstrably similar structure and function are said to be in the same protein family."},{"Start":"03:39.230 ","End":"03:44.240","Text":"A strong evolutionary relationship is usually evident within a protein family."},{"Start":"03:44.240 ","End":"03:47.270","Text":"For example, the globin family has"},{"Start":"03:47.270 ","End":"03:52.225","Text":"many different proteins with both structural and sequence similarity to myoglobin."},{"Start":"03:52.225 ","End":"03:55.790","Text":"2 or more families with little primary sequence similarity that use"},{"Start":"03:55.790 ","End":"04:00.935","Text":"the same major structural motif and have functional similarities are super families."},{"Start":"04:00.935 ","End":"04:05.990","Text":"Again, 2 or more families with little primary sequence similarity that use"},{"Start":"04:05.990 ","End":"04:09.320","Text":"the same major structural motif and have"},{"Start":"04:09.320 ","End":"04:14.500","Text":"functional similarities are considered super families."},{"Start":"04:14.500 ","End":"04:17.300","Text":"An evolutionary relationship between the families in"},{"Start":"04:17.300 ","End":"04:20.284","Text":"a super family is considered probable,"},{"Start":"04:20.284 ","End":"04:22.835","Text":"even though time and functional distinctions,"},{"Start":"04:22.835 ","End":"04:25.460","Text":"hence different adaptive pressures may have"},{"Start":"04:25.460 ","End":"04:28.550","Text":"erased many of the tail-tail sequence relationships."},{"Start":"04:28.550 ","End":"04:34.295","Text":"A protein family may be widespread in all 3 domains of cellular life."},{"Start":"04:34.295 ","End":"04:36.260","Text":"The bacteria, the archaea,"},{"Start":"04:36.260 ","End":"04:41.044","Text":"and the eukarya suggesting a very ancient origin."},{"Start":"04:41.044 ","End":"04:44.360","Text":"Other families may be present in only a small group of"},{"Start":"04:44.360 ","End":"04:48.140","Text":"organisms indicating that the structure arose more recently."},{"Start":"04:48.140 ","End":"04:53.450","Text":"Tracing the natural history of structural motifs using structural classifications provide"},{"Start":"04:53.450 ","End":"04:59.110","Text":"a powerful complement to sequence analysis in tracing many evolutionary relationships."},{"Start":"04:59.110 ","End":"05:02.570","Text":"Improve classification and comparison systems for"},{"Start":"05:02.570 ","End":"05:07.055","Text":"proteins led to the elucidation of new functional relationships."},{"Start":"05:07.055 ","End":"05:10.870","Text":"Given the central role of proteins in living organisms,"},{"Start":"05:10.870 ","End":"05:17.000","Text":"these structural comparisons can help illuminate every aspect of biochemistry from"},{"Start":"05:17.000 ","End":"05:19.310","Text":"the evolution of individual proteins to"},{"Start":"05:19.310 ","End":"05:23.510","Text":"the evolutionary history of complete metabolic pathways."},{"Start":"05:23.510 ","End":"05:26.030","Text":"With this, we completed the topic of"},{"Start":"05:26.030 ","End":"05:29.420","Text":"structural classification within protein structure,"},{"Start":"05:29.420 ","End":"05:33.110","Text":"and you should be able to talk about protein classification based"},{"Start":"05:33.110 ","End":"05:37.800","Text":"on structure and identify structure and evolutionary relationships."}],"ID":29589},{"Watched":false,"Name":"Exercise 13","Duration":"1m 22s","ChapterTopicVideoID":28344,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.890","Text":"We have an exercise testing on knowledge on structure classification."},{"Start":"00:04.890 ","End":"00:09.525","Text":"What are the 4 classes protein structures are divided into?"},{"Start":"00:09.525 ","End":"00:11.700","Text":"At the highest level of classification,"},{"Start":"00:11.700 ","End":"00:14.475","Text":"protein structures are divided into 4 classes."},{"Start":"00:14.475 ","End":"00:18.885","Text":"You have the all Alpha: These are structures that are made of all Alpha-helices,"},{"Start":"00:18.885 ","End":"00:21.270","Text":"and if you remember in the lesson itself,"},{"Start":"00:21.270 ","End":"00:24.600","Text":"we showed multiple figures of this."},{"Start":"00:24.600 ","End":"00:27.645","Text":"You have the all Beta forms."},{"Start":"00:27.645 ","End":"00:30.510","Text":"You have the Alpha over Beta in which"},{"Start":"00:30.510 ","End":"00:34.320","Text":"the Alpha and Beta segments are interspersed or alternate,"},{"Start":"00:34.320 ","End":"00:37.710","Text":"and you have the Alpha and Beta in which"},{"Start":"00:37.710 ","End":"00:41.505","Text":"the Alpha and B- regions are somewhat segregated."},{"Start":"00:41.505 ","End":"00:43.920","Text":"Again, you have all Alpha,"},{"Start":"00:43.920 ","End":"00:46.605","Text":"so these are protein structures that are made of all Alpha-helices."},{"Start":"00:46.605 ","End":"00:47.850","Text":"You have all Beta,"},{"Start":"00:47.850 ","End":"00:52.684","Text":"structures that are made of all Beta sheets, Beta forms."},{"Start":"00:52.684 ","End":"00:54.511","Text":"You have Alpha over Beta,"},{"Start":"00:54.511 ","End":"00:59.165","Text":"protein structures that have Alpha and Beta segments interspersed, alternating,"},{"Start":"00:59.165 ","End":"01:01.940","Text":"mixed together, or you have the fourth,"},{"Start":"01:01.940 ","End":"01:03.140","Text":"which is Alpha and Beta,"},{"Start":"01:03.140 ","End":"01:06.995","Text":"in which the Alpha and Beta regions are somewhat segregated."},{"Start":"01:06.995 ","End":"01:12.559","Text":"In each class are tens to hundreds of different folding arrangements,"},{"Start":"01:12.559 ","End":"01:16.070","Text":"built up from increasingly identifiable substructures."},{"Start":"01:16.070 ","End":"01:18.710","Text":"Some substructure arrangements are very common,"},{"Start":"01:18.710 ","End":"01:22.690","Text":"others have been found in just 1 protein."}],"ID":29590},{"Watched":false,"Name":"Exercise 14","Duration":"2m 19s","ChapterTopicVideoID":28345,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:06.015","Text":"Welcome to an exercise within the topic of structural classification."},{"Start":"00:06.015 ","End":"00:08.190","Text":"Proteins can be organized based on the presence"},{"Start":"00:08.190 ","End":"00:10.395","Text":"of the various motifs and their arrangements."},{"Start":"00:10.395 ","End":"00:12.825","Text":"Which statements in this regard are true?"},{"Start":"00:12.825 ","End":"00:16.275","Text":"A, the top 2 levels of organization,"},{"Start":"00:16.275 ","End":"00:19.350","Text":"class and fold are purely structural."},{"Start":"00:19.350 ","End":"00:21.920","Text":"B, below the fold level,"},{"Start":"00:21.920 ","End":"00:24.950","Text":"categorization is based on evolutionary relationships."},{"Start":"00:24.950 ","End":"00:29.180","Text":"C, many examples of recurring domain or motif structures reveal"},{"Start":"00:29.180 ","End":"00:34.000","Text":"that protein tertiary structure is not as conserved as protein primary sequence."},{"Start":"00:34.000 ","End":"00:38.510","Text":"D, the comparison of protein structures can provide information about evolution."},{"Start":"00:38.510 ","End":"00:41.630","Text":"E, A, B,"},{"Start":"00:41.630 ","End":"00:45.005","Text":"C and D. F A,"},{"Start":"00:45.005 ","End":"00:47.555","Text":"B and C. G A,"},{"Start":"00:47.555 ","End":"00:52.415","Text":"B and D. Let\u0027s go at this one at a time."},{"Start":"00:52.415 ","End":"00:56.374","Text":"The top 2 levels of organization class and fold,"},{"Start":"00:56.374 ","End":"01:00.739","Text":"our structural, therefore this is a true statement."},{"Start":"01:00.739 ","End":"01:03.950","Text":"B. Below the fold level,"},{"Start":"01:03.950 ","End":"01:07.145","Text":"categorization is based on evolutionary relationships."},{"Start":"01:07.145 ","End":"01:10.535","Text":"This is a true statement as well."},{"Start":"01:10.535 ","End":"01:13.350","Text":"You have class and fold that are structural,"},{"Start":"01:13.350 ","End":"01:18.335","Text":"and then below that you have evolutionary relationships."},{"Start":"01:18.335 ","End":"01:22.355","Text":"C. Many examples of recurring domain or motifs structures reveal"},{"Start":"01:22.355 ","End":"01:27.364","Text":"that protein tertiary structure is not as conserved as protein primary sequence."},{"Start":"01:27.364 ","End":"01:33.725","Text":"We actually mention that primary sequence seems to be less conserved."},{"Start":"01:33.725 ","End":"01:36.890","Text":"This sounds like it\u0027s incorrect."},{"Start":"01:36.890 ","End":"01:38.630","Text":"But let\u0027s keep on checking."},{"Start":"01:38.630 ","End":"01:43.865","Text":"D. The comparison of protein structures can provide information about evolution."},{"Start":"01:43.865 ","End":"01:50.795","Text":"This, we surely stated as a good way of giving us evolutionary information,"},{"Start":"01:50.795 ","End":"01:52.550","Text":"which leaves us with A, B,"},{"Start":"01:52.550 ","End":"01:53.780","Text":"and D being true,"},{"Start":"01:53.780 ","End":"01:55.010","Text":"C is not true,"},{"Start":"01:55.010 ","End":"02:01.625","Text":"so we can mark this off and it leaves us with G being the correct answer."},{"Start":"02:01.625 ","End":"02:04.830","Text":"So G is our correct answer."},{"Start":"02:04.830 ","End":"02:07.445","Text":"C would be correct if it said,"},{"Start":"02:07.445 ","End":"02:10.940","Text":"many examples of recurring domain or motif structures reveal"},{"Start":"02:10.940 ","End":"02:18.240","Text":"that protein tertiary structure is more reliably conserved than primary sequence."}],"ID":29591},{"Watched":false,"Name":"Exercise 15","Duration":"2m 11s","ChapterTopicVideoID":28346,"CourseChapterTopicPlaylistID":281856,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.885","Text":"Let\u0027s go into another question about structure classification."},{"Start":"00:03.885 ","End":"00:08.100","Text":"Define a protein, family and superfamily."},{"Start":"00:08.100 ","End":"00:12.480","Text":"Proteins with significant primary sequence similarity and/or with"},{"Start":"00:12.480 ","End":"00:15.150","Text":"demonstrably similar structure and/ or function are"},{"Start":"00:15.150 ","End":"00:18.540","Text":"said to be in the same protein family."},{"Start":"00:18.540 ","End":"00:25.460","Text":"Again, you have proteins that have significant primary sequence similarity or with"},{"Start":"00:25.460 ","End":"00:32.240","Text":"demonstrably similar structure and function are said to be in the same protein family."},{"Start":"00:32.240 ","End":"00:37.175","Text":"A strong evolutionary relationship is usually evident within a protein family."},{"Start":"00:37.175 ","End":"00:42.755","Text":"This explains this similar structure function or a primary sequence similarity."},{"Start":"00:42.755 ","End":"00:45.920","Text":"For example, the globin family has many different proteins"},{"Start":"00:45.920 ","End":"00:49.160","Text":"with both structural and sequence similarity to myoglobin."},{"Start":"00:49.160 ","End":"00:56.140","Text":"Subunit this is 1 unit versus the more complex hemoglobin that\u0027s made of 4 subunits,"},{"Start":"00:56.140 ","End":"00:59.900","Text":"2 or more families with little primary sequence similarity that sometimes make"},{"Start":"00:59.900 ","End":"01:04.430","Text":"use of the same major structural motif and half functional similarities,"},{"Start":"01:04.430 ","End":"01:07.955","Text":"these families are grouped as superfamilies."},{"Start":"01:07.955 ","End":"01:11.180","Text":"Once you have 2 or more families with"},{"Start":"01:11.180 ","End":"01:13.280","Text":"little primary sequence similarity that"},{"Start":"01:13.280 ","End":"01:16.940","Text":"sometimes makes use of the same major structural motif,"},{"Start":"01:16.940 ","End":"01:22.100","Text":"you have functional similarities these are grouped as super families."},{"Start":"01:22.100 ","End":"01:23.780","Text":"An evolutionary relationship between"},{"Start":"01:23.780 ","End":"01:26.540","Text":"the families in a superfamily is considered probable,"},{"Start":"01:26.540 ","End":"01:28.685","Text":"even though time and functional distinctions,"},{"Start":"01:28.685 ","End":"01:31.130","Text":"hence different adaptive pressures may have"},{"Start":"01:31.130 ","End":"01:34.960","Text":"erased many of the telltale sequence relationships."},{"Start":"01:34.960 ","End":"01:39.410","Text":"A protein family may be widespread in all 3 domains of cellular life,"},{"Start":"01:39.410 ","End":"01:41.210","Text":"the bacteria, Archaea and Eukarya,"},{"Start":"01:41.210 ","End":"01:43.685","Text":"suggesting a very ancient origin."},{"Start":"01:43.685 ","End":"01:47.030","Text":"While other families may be present in only a small group of"},{"Start":"01:47.030 ","End":"01:51.285","Text":"organisms indicating that the structure of rows more recently."},{"Start":"01:51.285 ","End":"01:55.100","Text":"If you remember thinking of an evolutionary tree."},{"Start":"01:55.100 ","End":"01:57.665","Text":"If you see these similarities,"},{"Start":"01:57.665 ","End":"02:01.220","Text":"they\u0027ve evolved more recently than if you compare"},{"Start":"02:01.220 ","End":"02:07.220","Text":"the similarities of where they\u0027ve come from, this and this."},{"Start":"02:07.220 ","End":"02:10.680","Text":"This is further back in time."}],"ID":29592}],"Thumbnail":null,"ID":281856}]

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