[{"Name":"Amino Acids","TopicPlaylistFirstVideoID":0,"Duration":null,"Videos":[{"Watched":false,"Name":"Introduction to Proteins","Duration":"4m 4s","ChapterTopicVideoID":27372,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.085","Text":"Hi, there. Welcome to amino acids."},{"Start":"00:02.085 ","End":"00:05.520","Text":"By the end of this section, you\u0027ll be able to describe the functions proteins have in"},{"Start":"00:05.520 ","End":"00:09.315","Text":"organisms and discuss the relationship between amino acids and protein."},{"Start":"00:09.315 ","End":"00:12.630","Text":"We had touched upon proteins in previous sections,"},{"Start":"00:12.630 ","End":"00:14.175","Text":"so some of this may be familiar."},{"Start":"00:14.175 ","End":"00:18.270","Text":"Proteins are the most abundant biological macro molecules."},{"Start":"00:18.270 ","End":"00:22.245","Text":"They are present in all cells and all parts of cells."},{"Start":"00:22.245 ","End":"00:25.800","Text":"Proteins mediate practically every process that takes place in"},{"Start":"00:25.800 ","End":"00:30.065","Text":"a cell exhibiting an almost endless diversity of functions."},{"Start":"00:30.065 ","End":"00:32.225","Text":"Proteins are found in great variety,"},{"Start":"00:32.225 ","End":"00:33.829","Text":"different types, and sizes."},{"Start":"00:33.829 ","End":"00:40.040","Text":"There are actually thousands of different kinds ranging in size"},{"Start":"00:40.040 ","End":"00:42.650","Text":"from relatively small peptides to huge polymers with"},{"Start":"00:42.650 ","End":"00:46.865","Text":"molecular weights in the millions may be found in a single cell."},{"Start":"00:46.865 ","End":"00:51.950","Text":"Furthermore, proteins exhibit enormous diversity of biological function and these are"},{"Start":"00:51.950 ","End":"00:53.420","Text":"the most important final products of"},{"Start":"00:53.420 ","End":"00:57.995","Text":"many information pathways that we will discuss in later lessons."},{"Start":"00:57.995 ","End":"01:02.765","Text":"Proteins are the molecular instruments through which genetic information is expressed."},{"Start":"01:02.765 ","End":"01:05.435","Text":"Relatively simple monomeric sub-units provide"},{"Start":"01:05.435 ","End":"01:08.665","Text":"the key to the structure of the thousand of different proteins."},{"Start":"01:08.665 ","End":"01:11.840","Text":"All proteins, whether from the most ancient lines of bacteria,"},{"Start":"01:11.840 ","End":"01:13.340","Text":"the simplest of bacteria,"},{"Start":"01:13.340 ","End":"01:15.230","Text":"or from the most complex forms of life,"},{"Start":"01:15.230 ","End":"01:21.845","Text":"including human beings, are constructed from the same ubiquitous set of 20 amino acids."},{"Start":"01:21.845 ","End":"01:26.390","Text":"These are covalently linked in characteristic linear sequences."},{"Start":"01:26.390 ","End":"01:31.565","Text":"Since each of these amino acids has a side chain with distinctive chemical properties,"},{"Start":"01:31.565 ","End":"01:36.440","Text":"this group of 20 precursor molecules may be regarded"},{"Start":"01:36.440 ","End":"01:42.235","Text":"as the alphabet in which the language of protein structure is written."},{"Start":"01:42.235 ","End":"01:46.355","Text":"These are the 20 amino acids in different forms."},{"Start":"01:46.355 ","End":"01:48.073","Text":"These are the same ones,"},{"Start":"01:48.073 ","End":"01:50.330","Text":"but in different depictions."},{"Start":"01:50.330 ","End":"01:54.180","Text":"This is the ball and chain model of glycine and"},{"Start":"01:54.180 ","End":"01:58.754","Text":"here you have molecular chemical biochemical representation,"},{"Start":"01:58.754 ","End":"02:00.365","Text":"so these are the same."},{"Start":"02:00.365 ","End":"02:02.690","Text":"What you see is the gray represents"},{"Start":"02:02.690 ","End":"02:06.305","Text":"carbon and there are two carbons here that are linked."},{"Start":"02:06.305 ","End":"02:12.740","Text":"You have red that represents oxygen,"},{"Start":"02:12.740 ","End":"02:16.655","Text":"and you have blue that represents nitrogen,"},{"Start":"02:16.655 ","End":"02:20.955","Text":"or basically the amine group,"},{"Start":"02:20.955 ","End":"02:24.635","Text":"so if you see different amine groups,"},{"Start":"02:24.635 ","End":"02:28.040","Text":"and then the white is the hydrogens."},{"Start":"02:28.040 ","End":"02:35.345","Text":"These 20 amino acids depicted in the two types of forms and these are interchangeable."},{"Start":"02:35.345 ","End":"02:37.250","Text":"These are the same."},{"Start":"02:37.250 ","End":"02:40.475","Text":"These are basically the alphabet,"},{"Start":"02:40.475 ","End":"02:42.890","Text":"the letters that make up the words,"},{"Start":"02:42.890 ","End":"02:45.395","Text":"with the words being protein."},{"Start":"02:45.395 ","End":"02:48.140","Text":"To generate a particular protein,"},{"Start":"02:48.140 ","End":"02:53.300","Text":"amino acids are covalently linked in 8 characteristic linear sequence."},{"Start":"02:53.300 ","End":"02:56.240","Text":"What is most remarkable is cells can produce"},{"Start":"02:56.240 ","End":"02:59.623","Text":"proteins with strikingly different properties,"},{"Start":"02:59.623 ","End":"03:01.340","Text":"and functions, and activities by joining"},{"Start":"03:01.340 ","End":"03:07.100","Text":"the same 2 amino acids in different combinations and sequences."},{"Start":"03:07.100 ","End":"03:08.240","Text":"From the building blocks,"},{"Start":"03:08.240 ","End":"03:11.780","Text":"different organisms can make such widely diverse products as"},{"Start":"03:11.780 ","End":"03:16.205","Text":"enzymes, hormones, antibodies, transporters,"},{"Start":"03:16.205 ","End":"03:21.350","Text":"muscle fibers, the lens protein of the eye, feathers, spider webs,"},{"Start":"03:21.350 ","End":"03:22.970","Text":"rhinoceros horn, milk proteins,"},{"Start":"03:22.970 ","End":"03:24.211","Text":"antibiotics, mushroom poisons,"},{"Start":"03:24.211 ","End":"03:28.415","Text":"and countless other substances having biological activities."},{"Start":"03:28.415 ","End":"03:32.135","Text":"Among these numerous protein products,"},{"Start":"03:32.135 ","End":"03:36.315","Text":"the enzymes are the most varied and specialized."},{"Start":"03:36.315 ","End":"03:40.607","Text":"Effectively, also the reactants are catalyzed by enzymes and,"},{"Start":"03:40.607 ","End":"03:44.950","Text":"therefore, require this variability and diversity."},{"Start":"03:44.950 ","End":"03:50.270","Text":"We will begin with a description of the fundamental chemical properties of amino acids,"},{"Start":"03:50.270 ","End":"03:53.570","Text":"peptides, and proteins throughout the chapter."},{"Start":"03:53.570 ","End":"03:58.280","Text":"By this point, you should be able to describe the general big picture function of"},{"Start":"03:58.280 ","End":"04:04.290","Text":"proteins in organisms and discuss the relationship between amino acids and protein."}],"ID":28485},{"Watched":false,"Name":"Exercise 1","Duration":"3m 43s","ChapterTopicVideoID":27373,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:07.065","Text":"Hi there. We are in an exercise covering the section of introduction to proteins."},{"Start":"00:07.065 ","End":"00:08.670","Text":"Which statement is false?"},{"Start":"00:08.670 ","End":"00:13.050","Text":"A, proteins are the most abundant biological macro molecules."},{"Start":"00:13.050 ","End":"00:15.300","Text":"B, there are thousands of"},{"Start":"00:15.300 ","End":"00:18.720","Text":"different kinds of proteins ranging in size, shape, and function."},{"Start":"00:18.720 ","End":"00:23.445","Text":"C, all proteins are constructed from 20 amino acids."},{"Start":"00:23.445 ","End":"00:29.400","Text":"D, enzymes are the least varied and specialized proteins."},{"Start":"00:29.400 ","End":"00:33.990","Text":"E, proteins are linear sequences of amino acids covalently linked together."},{"Start":"00:33.990 ","End":"00:40.640","Text":"Let\u0027s start with A. Proteins are the most abundant biological macro molecules."},{"Start":"00:40.640 ","End":"00:43.700","Text":"Talks about this early on in the course,"},{"Start":"00:43.700 ","End":"00:46.520","Text":"the first chapter, and in this section,"},{"Start":"00:46.520 ","End":"00:51.050","Text":"where proteins are biological macro molecules"},{"Start":"00:51.050 ","End":"00:55.425","Text":"and they are the most abundant biological macro molecules."},{"Start":"00:55.425 ","End":"00:58.490","Text":"This one is true, therefore,"},{"Start":"00:58.490 ","End":"01:03.499","Text":"it isn\u0027t the right answer because we\u0027re looking for what is false,"},{"Start":"01:03.499 ","End":"01:06.710","Text":"which statement is not true?"},{"Start":"01:06.710 ","End":"01:08.720","Text":"B, there are thousands of different kinds of"},{"Start":"01:08.720 ","End":"01:11.705","Text":"proteins ranging in size, shape, and function."},{"Start":"01:11.705 ","End":"01:16.170","Text":"If you recall, we mentioned that there are antibodies,"},{"Start":"01:16.170 ","End":"01:18.725","Text":"and enzymes, and muscle fibers,"},{"Start":"01:18.725 ","End":"01:20.128","Text":"and rhinoceros horn,"},{"Start":"01:20.128 ","End":"01:27.415","Text":"and so many different types of things that fall under the category of proteins."},{"Start":"01:27.415 ","End":"01:32.495","Text":"Yes, they range in size because the rhinoceros horn is huge"},{"Start":"01:32.495 ","End":"01:38.060","Text":"in comparison to an antibody that we can\u0027t even see because it\u0027s so small."},{"Start":"01:38.060 ","End":"01:41.930","Text":"They, most definitely, vary in shape."},{"Start":"01:41.930 ","End":"01:44.170","Text":"For example, an antibody."},{"Start":"01:44.170 ","End":"01:48.800","Text":"This is very different in shape from a feather or a spiderweb. B is true."},{"Start":"01:48.800 ","End":"01:50.363","Text":"B is true, therefore,"},{"Start":"01:50.363 ","End":"01:52.805","Text":"it can\u0027t be our answer because we\u0027re looking,"},{"Start":"01:52.805 ","End":"01:55.630","Text":"again, for something that is false."},{"Start":"01:55.630 ","End":"01:59.585","Text":"C. All proteins are constructed from 20 amino acids."},{"Start":"01:59.585 ","End":"02:05.450","Text":"Yes, we mentioned that there are 20 ubiquitous amino acids and different combinations of"},{"Start":"02:05.450 ","End":"02:07.940","Text":"these amino acids create and come"},{"Start":"02:07.940 ","End":"02:11.870","Text":"together to form the various different proteins we have."},{"Start":"02:11.870 ","End":"02:13.940","Text":"Once again, this is a true statement,"},{"Start":"02:13.940 ","End":"02:15.905","Text":"therefore this is not our statement."},{"Start":"02:15.905 ","End":"02:20.570","Text":"D. Enzymes are the least varied and specialized of proteins."},{"Start":"02:20.570 ","End":"02:27.425","Text":"But enzymes are what catalyze most reactions in organisms and in cells, therefore,"},{"Start":"02:27.425 ","End":"02:32.045","Text":"they need to be varied and diverse and,"},{"Start":"02:32.045 ","End":"02:34.880","Text":"therefore, are very specialized."},{"Start":"02:34.880 ","End":"02:39.485","Text":"Therefore, this sounds like it is"},{"Start":"02:39.485 ","End":"02:44.865","Text":"a false statement because they need to be on the higher variation,"},{"Start":"02:44.865 ","End":"02:49.760","Text":"so they are of the most varied and diverse and specialized of proteins."},{"Start":"02:49.760 ","End":"02:53.060","Text":"But let\u0027s check E. Proteins are linear sequences"},{"Start":"02:53.060 ","End":"02:56.284","Text":"of amino acids covalently linked together."},{"Start":"02:56.284 ","End":"03:01.055","Text":"Well, looking back at c where we said that basically all proteins,"},{"Start":"03:01.055 ","End":"03:05.023","Text":"whether from the most ancient lines of bacteria or from the most complex forms of life,"},{"Start":"03:05.023 ","End":"03:07.130","Text":"are constructed from the same ubiquitous set of"},{"Start":"03:07.130 ","End":"03:11.275","Text":"20 amino acids and how they are linked together."},{"Start":"03:11.275 ","End":"03:14.150","Text":"These types of bonds that we will later learn about"},{"Start":"03:14.150 ","End":"03:17.075","Text":"peptide bonds and these covalent bonds,"},{"Start":"03:17.075 ","End":"03:22.800","Text":"to form these linear sequences that then arrange into the different proteins."},{"Start":"03:22.800 ","End":"03:25.205","Text":"Well, this is a true statement, therefore,"},{"Start":"03:25.205 ","End":"03:28.280","Text":"it\u0027s not our answer and that leaves us with"},{"Start":"03:28.280 ","End":"03:32.210","Text":"D. Enzymes are the least varied and specialized of proteins."},{"Start":"03:32.210 ","End":"03:34.400","Text":"This means it\u0027s the false statement."},{"Start":"03:34.400 ","End":"03:36.890","Text":"If we want to make it a correct statement,"},{"Start":"03:36.890 ","End":"03:43.200","Text":"we would say enzymes are the most varied and specialized of proteins."}],"ID":28486},{"Watched":false,"Name":"Exercise 2","Duration":"44s","ChapterTopicVideoID":27374,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.160","Text":"Hi, there. Welcome to another exercise within the section of Introduction to Proteins."},{"Start":"00:05.160 ","End":"00:09.600","Text":"List at least 3 types of protein products made by organisms."},{"Start":"00:09.600 ","End":"00:14.354","Text":"We talked about amino acids being the building blocks that are used to make up proteins"},{"Start":"00:14.354 ","End":"00:19.770","Text":"and different organisms can use these building blocks to make widely diverse products,"},{"Start":"00:19.770 ","End":"00:23.250","Text":"such as enzymes, hormones,"},{"Start":"00:23.250 ","End":"00:28.333","Text":"antibodies, transporters, muscle fibers seen here,"},{"Start":"00:28.333 ","End":"00:30.750","Text":"the lens protein of feathers,"},{"Start":"00:30.750 ","End":"00:33.809","Text":"spider webs, rhinoceros horn, milk proteins, antibiotics,"},{"Start":"00:33.809 ","End":"00:41.260","Text":"mushrooms, poisons, and countless other substances having distinct biological activities."}],"ID":28487},{"Watched":false,"Name":"Amino Acids","Duration":"12m 56s","ChapterTopicVideoID":27375,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.400","Text":"Welcome to the topic of amino acids,"},{"Start":"00:02.400 ","End":"00:04.590","Text":"where we\u0027ll be talking about amino acids."},{"Start":"00:04.590 ","End":"00:08.010","Text":"In this lesson, we will learn about the common structural features of amino acids"},{"Start":"00:08.010 ","End":"00:12.090","Text":"and naming and codon identification of amino acids."},{"Start":"00:12.090 ","End":"00:15.405","Text":"Amino acids protein architecture."},{"Start":"00:15.405 ","End":"00:18.540","Text":"Proteins are polymers of amino acids with"},{"Start":"00:18.540 ","End":"00:24.150","Text":"each amino acid residue joined to its neighbor by a specific type of covalent bond."},{"Start":"00:24.150 ","End":"00:26.535","Text":"Let\u0027s introduce this term I just mentioned,"},{"Start":"00:26.535 ","End":"00:29.400","Text":"an amino acid residue."},{"Start":"00:29.400 ","End":"00:31.850","Text":"It basically reflects the loss of the elements of"},{"Start":"00:31.850 ","End":"00:35.330","Text":"water when 1 amino acid is joined to another."},{"Start":"00:35.330 ","End":"00:37.490","Text":"Proteins can be broken down,"},{"Start":"00:37.490 ","End":"00:41.000","Text":"hydrolyzed, the term indicating water molecules are added."},{"Start":"00:41.000 ","End":"00:43.130","Text":"In order to do this, hydrolyzed,"},{"Start":"00:43.130 ","End":"00:48.590","Text":"we have hydro equals water."},{"Start":"00:48.590 ","End":"00:56.690","Text":"Hydrolyzed means that the water molecule was added in order to do this."},{"Start":"00:56.690 ","End":"00:58.460","Text":"Proteins can be broken down,"},{"Start":"00:58.460 ","End":"01:04.625","Text":"hydrolyzed to their constituent amino acids by a variety of methods."},{"Start":"01:04.625 ","End":"01:08.570","Text":"If you see here, we\u0027ve got amino acid and another amino acid,"},{"Start":"01:08.570 ","End":"01:12.430","Text":"and there is this association,"},{"Start":"01:12.430 ","End":"01:18.335","Text":"this interaction which results in these two,"},{"Start":"01:18.335 ","End":"01:20.135","Text":"as you see marked here,"},{"Start":"01:20.135 ","End":"01:25.205","Text":"coming together and this being removed."},{"Start":"01:25.205 ","End":"01:26.660","Text":"This is our water molecule,"},{"Start":"01:26.660 ","End":"01:30.995","Text":"the hydrogen from 1 amino acid and the OH from the other amino acid,"},{"Start":"01:30.995 ","End":"01:37.550","Text":"and then the nitrogen bonds with the carbon."},{"Start":"01:37.550 ","End":"01:40.760","Text":"This bond that H was detached,"},{"Start":"01:40.760 ","End":"01:46.280","Text":"this extra bond now will bond with the C while this bond is"},{"Start":"01:46.280 ","End":"01:52.340","Text":"broken and will bond with the H. Now you have the nitrogen carbon bound together."},{"Start":"01:52.340 ","End":"01:58.040","Text":"This is our peptide bond and water is released."},{"Start":"01:58.040 ","End":"02:01.160","Text":"This is a bond that forms between the 2 amino acids"},{"Start":"02:01.160 ","End":"02:04.580","Text":"with the nitrogen forming a bond with the carbon."},{"Start":"02:04.580 ","End":"02:07.335","Text":"This is a peptide bond."},{"Start":"02:07.335 ","End":"02:11.711","Text":"A peptide is between the 2 amino acids coming together with this peptide bond."},{"Start":"02:11.711 ","End":"02:12.986","Text":"It is a dipeptide,"},{"Start":"02:12.986 ","End":"02:14.378","Text":"di is for 2,"},{"Start":"02:14.378 ","End":"02:17.750","Text":"with 1 water molecule released between."},{"Start":"02:17.750 ","End":"02:23.030","Text":"Protein synthesis consumes more of a cell\u0027s energy than any other metabolic process"},{"Start":"02:23.030 ","End":"02:29.260","Text":"in trying to create the 20 different amino acids are commonly found in proteins."},{"Start":"02:29.260 ","End":"02:33.955","Text":"The first to be discovered was asparagine in 1806."},{"Start":"02:33.955 ","End":"02:38.125","Text":"The last of the 20 to be found was threonine,"},{"Start":"02:38.125 ","End":"02:42.415","Text":"and it was only identified over a century later in 1938."},{"Start":"02:42.415 ","End":"02:48.220","Text":"You have the first one discovered in 1806 and the last of the 20 discovered in 1938."},{"Start":"02:48.220 ","End":"02:52.630","Text":"All the amino acids have a trivial or common names."},{"Start":"02:52.630 ","End":"02:57.130","Text":"In some cases, they\u0027re derived from the source from which they were first isolated."},{"Start":"02:57.130 ","End":"02:59.590","Text":"As an example of asparagine,"},{"Start":"02:59.590 ","End":"03:02.050","Text":"which was first found in asparagus."},{"Start":"03:02.050 ","End":"03:04.690","Text":"This is our amino acid."},{"Start":"03:04.690 ","End":"03:06.745","Text":"This, of course, as you see,"},{"Start":"03:06.745 ","End":"03:09.388","Text":"it was found in asparagus,"},{"Start":"03:09.388 ","End":"03:12.275","Text":"and glutamate or glutamine,"},{"Start":"03:12.275 ","End":"03:15.725","Text":"which was initially found in wheat gluten."},{"Start":"03:15.725 ","End":"03:18.905","Text":"Tyrosine was first isolated from cheese."},{"Start":"03:18.905 ","End":"03:20.600","Text":"You see tyrosine here."},{"Start":"03:20.600 ","End":"03:26.120","Text":"It\u0027s a name, it\u0027s derived from the Greek word Tyros,"},{"Start":"03:26.120 ","End":"03:27.980","Text":"which means cheese,"},{"Start":"03:27.980 ","End":"03:32.735","Text":"and glycine, Greek for Glykos you see in here,"},{"Start":"03:32.735 ","End":"03:38.390","Text":"which means sweet and was so named because of its sweet taste."},{"Start":"03:38.390 ","End":"03:41.885","Text":"Amino acids share common structural features."},{"Start":"03:41.885 ","End":"03:47.252","Text":"All 20 of the common amino acids are Alpha amino acids."},{"Start":"03:47.252 ","End":"03:49.280","Text":"They have a carboxyl group and"},{"Start":"03:49.280 ","End":"03:54.905","Text":"an amino group bonded to the same carbon atom, the Alpha carbon."},{"Start":"03:54.905 ","End":"03:56.615","Text":"This is the carboxyl group,"},{"Start":"03:56.615 ","End":"03:58.205","Text":"and this is the amine group."},{"Start":"03:58.205 ","End":"04:01.655","Text":"So carboxyl and amino group."},{"Start":"04:01.655 ","End":"04:07.910","Text":"They\u0027re both bonded to the Alpha carbon."},{"Start":"04:07.910 ","End":"04:12.065","Text":"Now, each amino acid has an amino group, NH_2,"},{"Start":"04:12.065 ","End":"04:14.720","Text":"NH_3 plus, and this carboxyl group,"},{"Start":"04:14.720 ","End":"04:18.047","Text":"the COH or COO minus."},{"Start":"04:18.047 ","End":"04:22.130","Text":"Polypeptides are formed when the amino group of"},{"Start":"04:22.130 ","End":"04:29.075","Text":"1 amino acid forms an amide bond with the carboxyl group,"},{"Start":"04:29.075 ","End":"04:33.455","Text":"COOH, of another amino acid."},{"Start":"04:33.455 ","End":"04:38.440","Text":"Now, this reaction is catalyzed by ribosomes and generates 1 water molecule."},{"Start":"04:38.440 ","End":"04:39.935","Text":"What we have here,"},{"Start":"04:39.935 ","End":"04:42.290","Text":"as mentioned before, you have the H,"},{"Start":"04:42.290 ","End":"04:47.585","Text":"the hydrogen, and the hydrogen and the oxygen are extracted."},{"Start":"04:47.585 ","End":"04:50.345","Text":"This is the water molecule that\u0027s formed."},{"Start":"04:50.345 ","End":"04:55.489","Text":"This hydrogen is connected to this oxygen and then you have what you see here,"},{"Start":"04:55.489 ","End":"05:02.660","Text":"this peptide bond where the carboxyl group is now attached to the amid."},{"Start":"05:02.660 ","End":"05:06.575","Text":"Now, when we talk about this term amino acid,"},{"Start":"05:06.575 ","End":"05:10.310","Text":"you have, this is where the amino comes,"},{"Start":"05:10.310 ","End":"05:14.780","Text":"this term and this is where the acid,"},{"Start":"05:14.780 ","End":"05:23.764","Text":"because it donates the proton in order to make this amino acid."},{"Start":"05:23.764 ","End":"05:26.480","Text":"This is where the term was derived from,"},{"Start":"05:26.480 ","End":"05:33.515","Text":"just as an FYI to be a hint for you as to what constitutes an amino acid."},{"Start":"05:33.515 ","End":"05:37.130","Text":"They differ from each other in their side chains,"},{"Start":"05:37.130 ","End":"05:40.010","Text":"which are termed R groups."},{"Start":"05:40.010 ","End":"05:42.515","Text":"These various structures, size,"},{"Start":"05:42.515 ","End":"05:49.950","Text":"and electric charge and these influence the solubility of the amino acids in water."},{"Start":"05:49.950 ","End":"05:57.950","Text":"The general structure of this amino acid is common to all but 1 of the Alpha amino acids,"},{"Start":"05:57.950 ","End":"06:03.118","Text":"which is proline, acyclic amino acid and it is the exception."},{"Start":"06:03.118 ","End":"06:04.930","Text":"The R group or side-chain,"},{"Start":"06:04.930 ","End":"06:06.300","Text":"see here in this pink,"},{"Start":"06:06.300 ","End":"06:08.760","Text":"is attached to the Alpha carbon,"},{"Start":"06:08.760 ","End":"06:10.310","Text":"see in blue,"},{"Start":"06:10.310 ","End":"06:13.310","Text":"and is different in each amino acid."},{"Start":"06:13.310 ","End":"06:15.200","Text":"In addition to these 20 amino acids,"},{"Start":"06:15.200 ","End":"06:17.225","Text":"there are many less common ones."},{"Start":"06:17.225 ","End":"06:21.875","Text":"Some are residues modified after a protein has been synthesized."},{"Start":"06:21.875 ","End":"06:25.670","Text":"Other are amino acids present in living organisms,"},{"Start":"06:25.670 ","End":"06:29.300","Text":"but not as constituent elements of proteins."},{"Start":"06:29.300 ","End":"06:32.480","Text":"The common amino acids of proteins have been assigned"},{"Start":"06:32.480 ","End":"06:35.930","Text":"a three-letter abbreviations and one-letter symbols,"},{"Start":"06:35.930 ","End":"06:38.780","Text":"which are used as shorthand to indicate the composition"},{"Start":"06:38.780 ","End":"06:41.945","Text":"and sequence of amino acids polymerised and proteins."},{"Start":"06:41.945 ","End":"06:45.140","Text":"As you see in the figure below, the structure,"},{"Start":"06:45.140 ","End":"06:48.829","Text":"you have the three-letter symbols in a chain."},{"Start":"06:48.829 ","End":"06:53.810","Text":"This is representing either a polymer or a polypeptide, or a protein."},{"Start":"06:53.810 ","End":"06:56.980","Text":"Basically, it\u0027s an amino acid chain."},{"Start":"06:56.980 ","End":"07:01.445","Text":"These 3 letters represents an amino acid."},{"Start":"07:01.445 ","End":"07:03.169","Text":"This is the shorthand."},{"Start":"07:03.169 ","End":"07:05.345","Text":"Now, if you look at the figure on the right,"},{"Start":"07:05.345 ","End":"07:12.545","Text":"you see all the different amino acids as there are differentiated in the R groups."},{"Start":"07:12.545 ","End":"07:14.690","Text":"This figure highlights the differences in"},{"Start":"07:14.690 ","End":"07:17.885","Text":"the R groups that differentiate the amino acids."},{"Start":"07:17.885 ","End":"07:24.065","Text":"You see their full names as well as the abbreviations beneath in parenthesis,"},{"Start":"07:24.065 ","End":"07:26.210","Text":"of the three-letter symbol or the one."},{"Start":"07:26.210 ","End":"07:29.135","Text":"If you look at this chain here, you have,"},{"Start":"07:29.135 ","End":"07:33.620","Text":"the first one is S-E-R, this is serine."},{"Start":"07:33.620 ","End":"07:43.415","Text":"This can also be labeled with the one-letter symbol of S. If you see in the figure here,"},{"Start":"07:43.415 ","End":"07:45.500","Text":"the R groups that differentiate,"},{"Start":"07:45.500 ","End":"07:48.650","Text":"that distinguish the amino acids from each other."},{"Start":"07:48.650 ","End":"07:52.804","Text":"This portion is in different colors and indicated."},{"Start":"07:52.804 ","End":"08:02.060","Text":"Below it, you have the abbreviated one-letter or three-letter assignment per amino acid."},{"Start":"08:02.060 ","End":"08:07.745","Text":"We started this amino acid chain with serine and the three-letter symbol."},{"Start":"08:07.745 ","End":"08:09.920","Text":"You can also do the single letter symbol."},{"Start":"08:09.920 ","End":"08:13.555","Text":"Then we have valine over here."},{"Start":"08:13.555 ","End":"08:20.120","Text":"V-A-L also can be labeled with V. In this chain we,"},{"Start":"08:20.120 ","End":"08:21.950","Text":"have SV or serine or valine,"},{"Start":"08:21.950 ","End":"08:26.415","Text":"or S-E-R, V-A-L. Next you have leucine."},{"Start":"08:26.415 ","End":"08:31.175","Text":"Leucine, we see over here that is marked with L-E-U or L,"},{"Start":"08:31.175 ","End":"08:32.750","Text":"and so on and so forth."},{"Start":"08:32.750 ","End":"08:35.030","Text":"You have this chain. I\u0027ll go on."},{"Start":"08:35.030 ","End":"08:37.355","Text":"You have methionine, M-E-T,"},{"Start":"08:37.355 ","End":"08:40.100","Text":"methionine or M,"},{"Start":"08:40.100 ","End":"08:41.540","Text":"so on and so forth."},{"Start":"08:41.540 ","End":"08:47.330","Text":"Here, you have the one-letter abbreviation of the same notation of"},{"Start":"08:47.330 ","End":"08:53.435","Text":"a three-letter abbreviation that denotes the amino acids that are signified."},{"Start":"08:53.435 ","End":"08:56.600","Text":"Let\u0027s go into the naming convention of amino acids."},{"Start":"08:56.600 ","End":"08:58.160","Text":"We briefly touched up on it,"},{"Start":"08:58.160 ","End":"09:02.465","Text":"but let\u0027s go into the systematic convention."},{"Start":"09:02.465 ","End":"09:07.370","Text":"The abbreviations consists of the first three letters of the amino acid name."},{"Start":"09:07.370 ","End":"09:09.035","Text":"The one-letter code,"},{"Start":"09:09.035 ","End":"09:10.400","Text":"which was devised by"},{"Start":"09:10.400 ","End":"09:14.450","Text":"Margaret Oakley DayHoff who many consider the founder of bioinformatics,"},{"Start":"09:14.450 ","End":"09:19.460","Text":"which is a field of studying biology through information systems,"},{"Start":"09:19.460 ","End":"09:26.180","Text":"and it\u0027s actually of studying sequences of either genetic information or amino acids."},{"Start":"09:26.180 ","End":"09:28.010","Text":"It\u0027s similar to coding in a way,"},{"Start":"09:28.010 ","End":"09:30.724","Text":"but using genetic sequences."},{"Start":"09:30.724 ","End":"09:35.225","Text":"The one-letter code was designed to be easily memorized."},{"Start":"09:35.225 ","End":"09:38.090","Text":"6 amino acids have a unique first letter,"},{"Start":"09:38.090 ","End":"09:40.430","Text":"meaning they are the only amino acids that"},{"Start":"09:40.430 ","End":"09:44.930","Text":"have this letter as the first letter in the name."},{"Start":"09:44.930 ","End":"09:49.820","Text":"That is C-H-I-M-S-V and it is actually cysteine,"},{"Start":"09:49.820 ","End":"09:52.850","Text":"histidine, and you can look up the rest."},{"Start":"09:52.850 ","End":"09:56.180","Text":"For 5 more, 5 other amino acids,"},{"Start":"09:56.180 ","End":"10:00.425","Text":"the first letter of their name is not unique,"},{"Start":"10:00.425 ","End":"10:05.356","Text":"but the letter is assigned to the most common in the proteins."},{"Start":"10:05.356 ","End":"10:10.010","Text":"Let\u0027s say there are 2 amino acids that have the letter A."},{"Start":"10:10.010 ","End":"10:15.260","Text":"How it\u0027s decided which will actually be designated with A as"},{"Start":"10:15.260 ","End":"10:21.620","Text":"its single letter symbol is based on how common it\u0027s found in proteins."},{"Start":"10:21.620 ","End":"10:25.010","Text":"The one that\u0027s most prevalent in proteins,"},{"Start":"10:25.010 ","End":"10:28.985","Text":"it will be designated with an A."},{"Start":"10:28.985 ","End":"10:34.550","Text":"You have A-G-L-P-T. For example,"},{"Start":"10:34.550 ","End":"10:39.530","Text":"leucine is more common than lysine."},{"Start":"10:39.530 ","End":"10:42.870","Text":"Therefore, leucine is designated with the L. While"},{"Start":"10:42.870 ","End":"10:47.525","Text":"lysine is with a K. For another 4 amino acids,"},{"Start":"10:47.525 ","End":"10:50.315","Text":"they have a phonetically suggestive symbol."},{"Start":"10:50.315 ","End":"10:52.971","Text":"Phonetically, it\u0027s from hearing."},{"Start":"10:52.971 ","End":"10:54.500","Text":"Think of the word phone."},{"Start":"10:54.500 ","End":"10:56.615","Text":"You hear on a phone."},{"Start":"10:56.615 ","End":"10:58.145","Text":"You listen on a phone."},{"Start":"10:58.145 ","End":"11:03.350","Text":"These are R-F-Y-W. What is the phonetic?"},{"Start":"11:03.350 ","End":"11:04.580","Text":"You\u0027ve arginine."},{"Start":"11:04.580 ","End":"11:07.610","Text":"It sounds like it starts with an R. So arginine."},{"Start":"11:07.610 ","End":"11:10.610","Text":"You have F for phenylalanine."},{"Start":"11:10.610 ","End":"11:14.690","Text":"Even though phenylalanine is spelled with ph."},{"Start":"11:14.690 ","End":"11:22.355","Text":"Ph sounds like F. So it\u0027s phenylalanine with an F. Y, you have tyrosine."},{"Start":"11:22.355 ","End":"11:25.010","Text":"Well, we already have a T up here."},{"Start":"11:25.010 ","End":"11:31.280","Text":"Tyrosine, this is the specialty I of the Y stands out."},{"Start":"11:31.280 ","End":"11:32.900","Text":"So it was designated with a Y."},{"Start":"11:32.900 ","End":"11:38.389","Text":"Then you have tryptophan and it\u0027s basically like Elmer Fudd,"},{"Start":"11:38.389 ","End":"11:44.285","Text":"be very quiet, we\u0027re hunting twiptophan."},{"Start":"11:44.285 ","End":"11:47.450","Text":"It\u0027s actually trytophan with an R,"},{"Start":"11:47.450 ","End":"11:55.175","Text":"but said, I don\u0027t know how this was decided, but twiptophan."},{"Start":"11:55.175 ","End":"11:57.710","Text":"If you don\u0027t know who Elmer Fudd is,"},{"Start":"11:57.710 ","End":"12:01.325","Text":"well, it\u0027s the guy who\u0027s hunting rabbits."},{"Start":"12:01.325 ","End":"12:03.620","Text":"The rest were more difficult to assign."},{"Start":"12:03.620 ","End":"12:06.110","Text":"You have 4 amino acids that were assigned letters"},{"Start":"12:06.110 ","End":"12:09.125","Text":"found within are suggested by their names."},{"Start":"12:09.125 ","End":"12:14.550","Text":"You have D-N-E-Q and that goes with aspardic,"},{"Start":"12:14.550 ","End":"12:19.330","Text":"asparagine, glutamete, and qtamine."},{"Start":"12:19.330 ","End":"12:20.900","Text":"The last remaining one,"},{"Start":"12:20.900 ","End":"12:27.450","Text":"which we mentioned before in reference to leucine, is lysine."},{"Start":"12:27.450 ","End":"12:32.075","Text":"The letter chosen for it was the one closest to L,"},{"Start":"12:32.075 ","End":"12:34.475","Text":"and that is K,"},{"Start":"12:34.475 ","End":"12:38.760","Text":"because you have an alphabet A, B,"},{"Start":"12:38.760 ","End":"12:39.960","Text":"C, D, E, F, G, H, I, J,"},{"Start":"12:39.960 ","End":"12:43.410","Text":"K, L is next."},{"Start":"12:43.410 ","End":"12:47.220","Text":"That\u0027s how K was chosen for lysine."},{"Start":"12:47.220 ","End":"12:49.400","Text":"At this point, we completed the section"},{"Start":"12:49.400 ","End":"12:51.470","Text":"and we learned about the common structural features of"},{"Start":"12:51.470 ","End":"12:57.480","Text":"amino acids and the naming a codon identification of amino acids."}],"ID":28488},{"Watched":false,"Name":"Exercise 3","Duration":"1m 38s","ChapterTopicVideoID":27376,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.085","Text":"We\u0027re going to go over an exercise about amino acids."},{"Start":"00:04.085 ","End":"00:07.655","Text":"The 20 common amino acids share certain structural features."},{"Start":"00:07.655 ","End":"00:11.130","Text":"Mentioned at least 2 as were mentioned in the lesson."},{"Start":"00:11.130 ","End":"00:14.430","Text":"All the 20 common amino acids are Alpha-amino acids,"},{"Start":"00:14.430 ","End":"00:16.140","Text":"which means they have a carboxyl group,"},{"Start":"00:16.140 ","End":"00:18.525","Text":"a COOH, and an amino group,"},{"Start":"00:18.525 ","End":"00:22.710","Text":"an NH_2, bonded to the same carbon atom, the Alpha-carbon."},{"Start":"00:22.710 ","End":"00:25.380","Text":"They differ from each other in their side chains,"},{"Start":"00:25.380 ","End":"00:27.210","Text":"which are also known as R groups,"},{"Start":"00:27.210 ","End":"00:29.640","Text":"and these vary in structure, size,"},{"Start":"00:29.640 ","End":"00:30.660","Text":"and electric charge,"},{"Start":"00:30.660 ","End":"00:34.410","Text":"and influence the solubility of the amino acids in water."},{"Start":"00:34.410 ","End":"00:37.115","Text":"The common amino acids of proteins have been assigned"},{"Start":"00:37.115 ","End":"00:40.670","Text":"3-letter abbreviations and 1-letter symbols as seen"},{"Start":"00:40.670 ","End":"00:43.940","Text":"here which are used as shorthand to indicate"},{"Start":"00:43.940 ","End":"00:48.125","Text":"the composition and sequence of amino acids polymerized in proteins,"},{"Start":"00:48.125 ","End":"00:52.200","Text":"meaning, taking these, tyracine for short,"},{"Start":"00:52.200 ","End":"01:00.765","Text":"3-letter abbreviation is TYR and the 1-letter is Y from tyracine."},{"Start":"01:00.765 ","End":"01:04.670","Text":"The significance of having this shorthand is when"},{"Start":"01:04.670 ","End":"01:09.620","Text":"looking at a polymer and 1 indicate the actual sequence."},{"Start":"01:09.620 ","End":"01:15.050","Text":"It is much more practical to have a 3-letter or 1-letter way to indicate."},{"Start":"01:15.050 ","End":"01:16.880","Text":"Here, if we have tyracine,"},{"Start":"01:16.880 ","End":"01:18.620","Text":"you have a TYR,"},{"Start":"01:18.620 ","End":"01:21.245","Text":"and if you have asparagine,"},{"Start":"01:21.245 ","End":"01:23.270","Text":"you have the ASP, etc."},{"Start":"01:23.270 ","End":"01:30.800","Text":"Furthermore, we can have this same thing as a sequence of 1-letters."},{"Start":"01:30.800 ","End":"01:33.755","Text":"That is just a few points mentioning"},{"Start":"01:33.755 ","End":"01:38.910","Text":"some common structural features found in the common amino acids."}],"ID":28489},{"Watched":false,"Name":"Exercise 4","Duration":"1m 39s","ChapterTopicVideoID":27377,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.290 ","End":"00:04.755","Text":"Here, we have another exercise within amino acids."},{"Start":"00:04.755 ","End":"00:07.352","Text":"Proteins are polymers of amino acids."},{"Start":"00:07.352 ","End":"00:11.520","Text":"Explain this and how the amino acids come together to form proteins."},{"Start":"00:11.520 ","End":"00:13.860","Text":"Proteins are polymers of amino acids,"},{"Start":"00:13.860 ","End":"00:19.110","Text":"with each amino acid residue joined to its neighbor by a specific type of covalent bond."},{"Start":"00:19.110 ","End":"00:22.500","Text":"An amino acid residue is one that has lost the elements of"},{"Start":"00:22.500 ","End":"00:26.355","Text":"water as a result of 1 amino acid being joined to the other."},{"Start":"00:26.355 ","End":"00:30.090","Text":"What happens is you have in each a proton,"},{"Start":"00:30.090 ","End":"00:33.405","Text":"a hydrogen from 1 amino acid,"},{"Start":"00:33.405 ","End":"00:37.425","Text":"and the OH from another one."},{"Start":"00:37.425 ","End":"00:44.880","Text":"These are the elements of water because together these form H_2O the water molecule."},{"Start":"00:44.880 ","End":"00:49.010","Text":"Now, the reverse of this is when proteins are broken down, hydrolyzed,"},{"Start":"00:49.010 ","End":"00:51.530","Text":"water molecules are added in order to allow"},{"Start":"00:51.530 ","End":"00:55.475","Text":"the separation of protein components to their constituent amino acids."},{"Start":"00:55.475 ","End":"00:57.100","Text":"Water is added."},{"Start":"00:57.100 ","End":"00:59.400","Text":"You have the H_2O."},{"Start":"00:59.400 ","End":"01:00.960","Text":"H_2O, again,"},{"Start":"01:00.960 ","End":"01:04.740","Text":"we have the hydrogen and the OH."},{"Start":"01:04.740 ","End":"01:06.718","Text":"These, basically,"},{"Start":"01:06.718 ","End":"01:09.890","Text":"are added to a protein,"},{"Start":"01:09.890 ","End":"01:17.465","Text":"to a polymer in order to break up the bond between 2 amino acid residues."},{"Start":"01:17.465 ","End":"01:19.405","Text":"Each amino acid has an amino group,"},{"Start":"01:19.405 ","End":"01:21.860","Text":"NH_2 and a carboxylic group, COOH group."},{"Start":"01:21.860 ","End":"01:24.395","Text":"Polypeptides are formed when the amino group of"},{"Start":"01:24.395 ","End":"01:28.550","Text":"1 amino acid forms an amide bond with the carboxyl group of another amino acid."},{"Start":"01:28.550 ","End":"01:33.665","Text":"This reaction is catalyzed by ribosomes and generates 1 water molecule."},{"Start":"01:33.665 ","End":"01:40.200","Text":"This, in essence, is the process of how amino acids come together and form proteins."}],"ID":28490},{"Watched":false,"Name":"Amino Acid Arrangement","Duration":"8m 45s","ChapterTopicVideoID":27378,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.490","Text":"Hey there, we\u0027re in the chapter of amino acids,"},{"Start":"00:02.490 ","End":"00:03.960","Text":"peptides and proteins,"},{"Start":"00:03.960 ","End":"00:07.710","Text":"and we are covering amino acid arrangement."},{"Start":"00:07.710 ","End":"00:09.735","Text":"By the end of this section, you will be able to"},{"Start":"00:09.735 ","End":"00:12.210","Text":"talk about the conventions used to identify the carbons"},{"Start":"00:12.210 ","End":"00:14.250","Text":"in an amino acid and the systems of"},{"Start":"00:14.250 ","End":"00:16.940","Text":"identifying configuration and arrangement of amino acid."},{"Start":"00:16.940 ","End":"00:19.845","Text":"For all the common amino acids except glycine,"},{"Start":"00:19.845 ","End":"00:24.588","Text":"the Alpha carbon is bonded to the 4 groups."},{"Start":"00:24.588 ","End":"00:27.570","Text":"1, a carboxyl group,"},{"Start":"00:27.570 ","End":"00:30.960","Text":"2, an amino group,"},{"Start":"00:30.960 ","End":"00:34.040","Text":"3, an R group,"},{"Start":"00:34.040 ","End":"00:38.390","Text":"which is what differs between each amino acid,"},{"Start":"00:38.390 ","End":"00:41.719","Text":"and 4, a hydrogen atom, which in glycine,"},{"Start":"00:41.719 ","End":"00:45.650","Text":"the R group is another hydrogen atom, meaning in glycine,"},{"Start":"00:45.650 ","End":"00:51.800","Text":"this would be an H. The Alpha carbon atom is thus a chiral center."},{"Start":"00:51.800 ","End":"00:54.860","Text":"Chiral center of an atom is the atom in a molecule that is"},{"Start":"00:54.860 ","End":"00:58.656","Text":"bonded to 4 different chemical species."},{"Start":"00:58.656 ","End":"01:00.470","Text":"But remember that a chemical species is"},{"Start":"01:00.470 ","End":"01:04.469","Text":"an atom or molecule with a specific molecular structure."},{"Start":"01:04.469 ","End":"01:06.945","Text":"Now, because of the tetrahedral arrangement"},{"Start":"01:06.945 ","End":"01:09.710","Text":"of the bonding orbitals around the Alpha carbon atom,"},{"Start":"01:09.710 ","End":"01:13.880","Text":"the 4 different groups can occupy 2 unique spatial arrangements,"},{"Start":"01:13.880 ","End":"01:18.125","Text":"and thus amino acids have 2 possible stereoisomers."},{"Start":"01:18.125 ","End":"01:21.020","Text":"A reminder from an earlier lesson,"},{"Start":"01:21.020 ","End":"01:27.300","Text":"since these 2 stereo isomers are non-superimposable mirror images of each other,"},{"Start":"01:27.300 ","End":"01:33.575","Text":"the 2 forms represents a class of stereoisomers called enantiomers."},{"Start":"01:33.575 ","End":"01:35.480","Text":"See the figure here,"},{"Start":"01:35.480 ","End":"01:39.812","Text":"you have an image and a mirror image."},{"Start":"01:39.812 ","End":"01:43.736","Text":"When they are not mirror images of each other,"},{"Start":"01:43.736 ","End":"01:47.730","Text":"they are, therefore, enantiomers."},{"Start":"01:47.730 ","End":"01:50.150","Text":"As a reminder, what makes"},{"Start":"01:50.150 ","End":"01:55.445","Text":"these mirror images for this versus this is that here this molecule,"},{"Start":"01:55.445 ","End":"01:59.240","Text":"based on the illustration is in front,"},{"Start":"01:59.240 ","End":"02:01.340","Text":"whereas based on this illustration,"},{"Start":"02:01.340 ","End":"02:02.753","Text":"this is in back."},{"Start":"02:02.753 ","End":"02:06.395","Text":"This, therefore, is not a mirror image,"},{"Start":"02:06.395 ","End":"02:13.335","Text":"meaning these cannot be fit one over the other in a superimposable way,"},{"Start":"02:13.335 ","End":"02:15.950","Text":"therefore, these are enantiomers."},{"Start":"02:15.950 ","End":"02:18.170","Text":"If you remember, we also explained that all molecules with"},{"Start":"02:18.170 ","End":"02:20.630","Text":"a chiral center are also optically active,"},{"Start":"02:20.630 ","End":"02:24.440","Text":"meaning they rotate the plane of plane polarized light affect"},{"Start":"02:24.440 ","End":"02:29.450","Text":"the refraction of light so that the angles by which the rays bend are not the same."},{"Start":"02:29.450 ","End":"02:31.028","Text":"In this figure,"},{"Start":"02:31.028 ","End":"02:35.450","Text":"you see stereoisomerism in Alpha amino acids."},{"Start":"02:35.450 ","End":"02:42.430","Text":"The 2 stereoisomers of alanine are L and D-Alanine,"},{"Start":"02:42.430 ","End":"02:47.896","Text":"and they are non-superimposable mirror images of each other, enantiomers."},{"Start":"02:47.896 ","End":"02:49.710","Text":"In b what you see,"},{"Start":"02:49.710 ","End":"02:51.163","Text":"and in c,"},{"Start":"02:51.163 ","End":"02:54.170","Text":"are 2 different conventions for showing the configuration in"},{"Start":"02:54.170 ","End":"02:57.485","Text":"space of stereoisomers in perspective formulas."},{"Start":"02:57.485 ","End":"03:01.527","Text":"If you have the ball and stick form here,"},{"Start":"03:01.527 ","End":"03:04.511","Text":"you\u0027re seeing 2 different representations."},{"Start":"03:04.511 ","End":"03:08.285","Text":"You have the solid wedge-shaped bonds"},{"Start":"03:08.285 ","End":"03:12.740","Text":"that project out of the plane of the paper so this is solid wedge,"},{"Start":"03:12.740 ","End":"03:15.200","Text":"that means it\u0027s in front."},{"Start":"03:15.200 ","End":"03:16.250","Text":"As you could see here,"},{"Start":"03:16.250 ","End":"03:20.720","Text":"these sticks seem like they\u0027re in front."},{"Start":"03:20.720 ","End":"03:24.695","Text":"While the dashed bonds that are inverted,"},{"Start":"03:24.695 ","End":"03:27.590","Text":"they show as if this is going back."},{"Start":"03:27.590 ","End":"03:29.660","Text":"This is behind the carbons."},{"Start":"03:29.660 ","End":"03:31.550","Text":"You could see this here as well."},{"Start":"03:31.550 ","End":"03:33.680","Text":"As with the sticks, you can\u0027t see where they go in."},{"Start":"03:33.680 ","End":"03:35.855","Text":"That means they are behind."},{"Start":"03:35.855 ","End":"03:38.262","Text":"Now in projection formulas,"},{"Start":"03:38.262 ","End":"03:44.030","Text":"we said that this is perspective formula,"},{"Start":"03:44.030 ","End":"03:48.360","Text":"this is ball and stick."},{"Start":"03:48.360 ","End":"03:55.100","Text":"Then what we see in c are actually projection formulas."},{"Start":"03:55.100 ","End":"04:00.740","Text":"The horizontal bonds are assumed to project out of the plane of the paper,"},{"Start":"04:00.740 ","End":"04:06.118","Text":"while the vertical bonds are assumed to be behind."},{"Start":"04:06.118 ","End":"04:10.730","Text":"However, projection formulas are often used casually and"},{"Start":"04:10.730 ","End":"04:15.575","Text":"are not always intended to portray a specific stereochemical configuration."},{"Start":"04:15.575 ","End":"04:24.530","Text":"Though the ideas we said that these are in front because they are horizontal,"},{"Start":"04:24.530 ","End":"04:30.305","Text":"while these are in back because they\u0027re vertical,"},{"Start":"04:30.305 ","End":"04:34.580","Text":"many times, this convention is not maintained."},{"Start":"04:34.580 ","End":"04:37.370","Text":"Special nomenclature has been developed to specify"},{"Start":"04:37.370 ","End":"04:42.560","Text":"the absolute configuration of the 4 substituents of asymmetric carbon atoms."},{"Start":"04:42.560 ","End":"04:45.920","Text":"The absolute configurations of simple sugars and amino acids are"},{"Start":"04:45.920 ","End":"04:49.245","Text":"specified by the D, L system."},{"Start":"04:49.245 ","End":"04:51.470","Text":"This was based on the configuration of"},{"Start":"04:51.470 ","End":"04:57.729","Text":"the 3-carbon sugar glyceraldehyde as proposed by Emil Fischer in 1891."},{"Start":"04:57.729 ","End":"04:59.740","Text":"For all chiral compounds,"},{"Start":"04:59.740 ","End":"05:02.590","Text":"stereoisomers having a configuration related to that of"},{"Start":"05:02.590 ","End":"05:05.500","Text":"the L-glyceraldehyde are designated L and"},{"Start":"05:05.500 ","End":"05:10.060","Text":"stereoisomers related to the D-glyceraldehyde"},{"Start":"05:10.060 ","End":"05:13.465","Text":"are designated D. The functional groups and as you see here,"},{"Start":"05:13.465 ","End":"05:18.433","Text":"L and D, the functional groups of L-Alanine are matched with those of"},{"Start":"05:18.433 ","End":"05:21.730","Text":"L-glyceraldehyde by aligning those that"},{"Start":"05:21.730 ","End":"05:25.570","Text":"can be interconverted by simple one-step chemical reaction."},{"Start":"05:25.570 ","End":"05:28.855","Text":"The carboxyl group of the L-Alanine"},{"Start":"05:28.855 ","End":"05:32.965","Text":"occupies the same position about the chiral carbon as does the aldehyde group"},{"Start":"05:32.965 ","End":"05:36.580","Text":"of the L-glyceraldehyde because an aldehyde is readily"},{"Start":"05:36.580 ","End":"05:40.510","Text":"converted to a carboxyl group via a 1-step oxidation."},{"Start":"05:40.510 ","End":"05:44.745","Text":"The aldehyde and L-glyceraldehyde,"},{"Start":"05:44.745 ","End":"05:50.423","Text":"it\u0027s found here in orientation to the other 3 bonds of the chiral center."},{"Start":"05:50.423 ","End":"05:52.820","Text":"If we had to reiterate what we just said,"},{"Start":"05:52.820 ","End":"05:55.235","Text":"you have the L-glyceraldehyde,"},{"Start":"05:55.235 ","End":"05:57.120","Text":"you have the L-Alanine."},{"Start":"05:57.120 ","End":"06:04.415","Text":"Basically, you have the aldehyde that is sitting at the same spot in relation"},{"Start":"06:04.415 ","End":"06:12.301","Text":"to the carbon so that it is therefore the L-Alanine where if you look here,"},{"Start":"06:12.301 ","End":"06:15.355","Text":"you see the CHO versus COO,"},{"Start":"06:15.355 ","End":"06:20.660","Text":"it\u0027s reversed so that the hydrogen now is here on the left and therefore,"},{"Start":"06:20.660 ","End":"06:23.510","Text":"the hydrogen here and the D-Alanine is on the left,"},{"Start":"06:23.510 ","End":"06:25.775","Text":"the amine group, and the hydroxyl group."},{"Start":"06:25.775 ","End":"06:30.050","Text":"Therefore, this is the D with the hydrogen over here,"},{"Start":"06:30.050 ","End":"06:31.677","Text":"therefore, it is the D-Alanine."},{"Start":"06:31.677 ","End":"06:34.969","Text":"There\u0027s another system of specifying configuration"},{"Start":"06:34.969 ","End":"06:38.515","Text":"around a chiral center in the RS system,"},{"Start":"06:38.515 ","End":"06:42.890","Text":"which is used in the systematic nomenclature of organic chemistry and describes"},{"Start":"06:42.890 ","End":"06:47.810","Text":"more precisely the configuration of molecules with more than one chiral center."},{"Start":"06:47.810 ","End":"06:53.475","Text":"The 2 conventions are used to identify the carbons in an amino acid,"},{"Start":"06:53.475 ","End":"06:55.545","Text":"a practice that can be confusing."},{"Start":"06:55.545 ","End":"06:59.810","Text":"The additional carbons and an R group are commonly designated with Greek letters."},{"Start":"06:59.810 ","End":"07:02.015","Text":"You have Beta, Gamma, Delta, Epsilon,"},{"Start":"07:02.015 ","End":"07:05.725","Text":"and so on proceeding out from the Alpha carbon."},{"Start":"07:05.725 ","End":"07:07.770","Text":"Alpha, Beta, Gamma,"},{"Start":"07:07.770 ","End":"07:09.470","Text":"Delta Epsilon like A,"},{"Start":"07:09.470 ","End":"07:12.770","Text":"B, C, D. For most other organic molecules,"},{"Start":"07:12.770 ","End":"07:17.740","Text":"carbon atoms are simply numbered from one end, giving highest priority,"},{"Start":"07:17.740 ","End":"07:25.385","Text":"C-1 to the carbon with the substituent containing the atom of highest atomic number."},{"Start":"07:25.385 ","End":"07:28.490","Text":"Substituent refers to an atom or group of atoms that"},{"Start":"07:28.490 ","End":"07:32.384","Text":"replaces another atom or group of atoms in a molecule."},{"Start":"07:32.384 ","End":"07:35.062","Text":"Within this ladder convention,"},{"Start":"07:35.062 ","End":"07:42.270","Text":"the carboxyl carbon would be C-1 and the Alpha carbon would be C-2."},{"Start":"07:42.270 ","End":"07:45.800","Text":"You have the carboxyl because this is one end and"},{"Start":"07:45.800 ","End":"07:49.160","Text":"that is C-1 and then you have Alpha carbon,"},{"Start":"07:49.160 ","End":"07:51.545","Text":"the central to the chiral group,"},{"Start":"07:51.545 ","End":"07:56.030","Text":"the chiral center as 2 or Alpha."},{"Start":"07:56.030 ","End":"07:58.978","Text":"The Alpha carbon would be 2."},{"Start":"07:58.978 ","End":"08:00.920","Text":"Then as you move on,"},{"Start":"08:00.920 ","End":"08:03.320","Text":"this is basically the R group,"},{"Start":"08:03.320 ","End":"08:10.080","Text":"and this R group consists of 4 or more carbons in the chain so they will be Number 3,"},{"Start":"08:10.080 ","End":"08:11.490","Text":"4, 5, 6."},{"Start":"08:11.490 ","End":"08:15.770","Text":"Or if we\u0027re looking at the Alpha carbon and the rest of the carbons and the R group,"},{"Start":"08:15.770 ","End":"08:18.710","Text":"it would be Beta, Gamma, Delta, Epsilon."},{"Start":"08:18.710 ","End":"08:23.780","Text":"In some cases, such as amino acids with heterocyclic R groups,"},{"Start":"08:23.780 ","End":"08:26.990","Text":"which means basically a circle or a ring."},{"Start":"08:26.990 ","End":"08:30.710","Text":"If this basically folded into a ring,"},{"Start":"08:30.710 ","End":"08:35.917","Text":"the Greek lettering system is ambiguous and the numbering convention is therefore used."},{"Start":"08:35.917 ","End":"08:39.590","Text":"At this point, you should understand the convention to use to identify the carbons in"},{"Start":"08:39.590 ","End":"08:41.390","Text":"an amino acid and the systems of"},{"Start":"08:41.390 ","End":"08:45.330","Text":"identifying configuration and arrangement of amino acids."}],"ID":28491},{"Watched":false,"Name":"Exercise 5","Duration":"1m 34s","ChapterTopicVideoID":27379,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.450","Text":"What did we learn within the topic of amino acid arrangement?"},{"Start":"00:03.450 ","End":"00:07.635","Text":"What are the 2 conventions used to identify the carbons in an amino acid?"},{"Start":"00:07.635 ","End":"00:12.790","Text":"The 2 conventions used to identify the carbons in amino acid are, 1,"},{"Start":"00:12.790 ","End":"00:18.355","Text":"in which the additional carbons in an R group are commonly designated with Greek letters."},{"Start":"00:18.355 ","End":"00:21.595","Text":"You start with Alpha for the original 1,"},{"Start":"00:21.595 ","End":"00:24.470","Text":"the chiral center 1, the Alpha carbon."},{"Start":"00:24.470 ","End":"00:26.415","Text":"Then you add Beta,"},{"Start":"00:26.415 ","End":"00:28.185","Text":"Gamma, Delta, Epsilon,"},{"Start":"00:28.185 ","End":"00:31.890","Text":"and so on proceeding out from the Alpha carbon."},{"Start":"00:31.890 ","End":"00:36.829","Text":"The second one is one where for other organic molecules,"},{"Start":"00:36.829 ","End":"00:40.355","Text":"carbon atoms are mostly numbered from one end,"},{"Start":"00:40.355 ","End":"00:43.550","Text":"giving highest priority C-1 to the carbon with"},{"Start":"00:43.550 ","End":"00:47.520","Text":"the substituent containing the atom of highest atomic number."},{"Start":"00:47.520 ","End":"00:50.330","Text":"To remind you, substituent refers to an atom or group of"},{"Start":"00:50.330 ","End":"00:53.960","Text":"atoms that replaces another atom or group of atoms in a molecule."},{"Start":"00:53.960 ","End":"00:58.673","Text":"It\u0027s saying you have the carbon, what\u0027s this?"},{"Start":"00:58.673 ","End":"01:03.100","Text":"2 oxygens, that will be designated, C-1."},{"Start":"01:03.100 ","End":"01:05.900","Text":"Within this latter convention,"},{"Start":"01:05.900 ","End":"01:11.405","Text":"the carboxyl carbon of the amino acid would be C-1,"},{"Start":"01:11.405 ","End":"01:14.600","Text":"and the Alpha carbon would be C-2."},{"Start":"01:14.600 ","End":"01:18.290","Text":"In some cases such as amino acids with heterocyclic R groups,"},{"Start":"01:18.290 ","End":"01:23.340","Text":"meaning that the R group is actually cyclic,"},{"Start":"01:23.340 ","End":"01:26.505","Text":"so let\u0027s say it would be like this,"},{"Start":"01:26.505 ","End":"01:28.295","Text":"this is the R group."},{"Start":"01:28.295 ","End":"01:34.440","Text":"The Greek lettering system is ambiguous and the numbering convention is therefore used."}],"ID":28492},{"Watched":false,"Name":"Exercise 6","Duration":"36s","ChapterTopicVideoID":27380,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.955","Text":"Hi there. Welcome back to amino acid arrangement."},{"Start":"00:02.955 ","End":"00:05.879","Text":"For all the common amino acids except glycine,"},{"Start":"00:05.879 ","End":"00:10.125","Text":"the Alpha carbon is bonded to 4 different groups. List these."},{"Start":"00:10.125 ","End":"00:12.465","Text":"As mentioned, the common amino acids,"},{"Start":"00:12.465 ","End":"00:14.775","Text":"the Alpha carbon bonded to;"},{"Start":"00:14.775 ","End":"00:18.045","Text":"a carboxyl group, an amino group,"},{"Start":"00:18.045 ","End":"00:24.975","Text":"an R group and this changes and is the different aspect of the different amino acids,"},{"Start":"00:24.975 ","End":"00:27.330","Text":"and a hydrogen atom."},{"Start":"00:27.330 ","End":"00:34.410","Text":"Whereas in glycine, the R group is just another hydrogen atom and therefore,"},{"Start":"00:34.410 ","End":"00:36.610","Text":"it is the exception."}],"ID":28493},{"Watched":false,"Name":"Exercise 7","Duration":"1m 25s","ChapterTopicVideoID":27381,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.210","Text":"Within amino acid arrangement,"},{"Start":"00:03.210 ","End":"00:07.170","Text":"what is the term that defines the Alpha-amino acids?"},{"Start":"00:07.170 ","End":"00:10.395","Text":"All the common amino acids except glycine,"},{"Start":"00:10.395 ","End":"00:12.690","Text":"and we have the Alpha-amino acids,"},{"Start":"00:12.690 ","End":"00:16.065","Text":"have 4 different groups bonded to their Alpha-carbon."},{"Start":"00:16.065 ","End":"00:17.670","Text":"This is the Alpha-carbon."},{"Start":"00:17.670 ","End":"00:20.025","Text":"Which means it is a chiral center."},{"Start":"00:20.025 ","End":"00:23.040","Text":"As a reminder, a chiral center of an atom is the atom in"},{"Start":"00:23.040 ","End":"00:25.890","Text":"the molecule that is bonded to 4 different chemical species."},{"Start":"00:25.890 ","End":"00:31.710","Text":"You have 1, 2, 3, 4. 4 chemical species."},{"Start":"00:31.710 ","End":"00:33.360","Text":"What is a chemical species?"},{"Start":"00:33.360 ","End":"00:38.175","Text":"That is basically any atom or molecule with a specific molecular structure."},{"Start":"00:38.175 ","End":"00:40.935","Text":"This brings it all to say,"},{"Start":"00:40.935 ","End":"00:43.675","Text":"4 different groups bonded to their Alpha-carbon,"},{"Start":"00:43.675 ","End":"00:45.890","Text":"with the R group being different between them."},{"Start":"00:45.890 ","End":"00:50.595","Text":"So in all of them, you can find this central Alpha-carbon,"},{"Start":"00:50.595 ","End":"00:53.505","Text":"that has the COO,"},{"Start":"00:53.505 ","End":"00:57.390","Text":"1, the hydrogen, 2,"},{"Start":"00:57.390 ","End":"01:00.180","Text":"the amine, 3,"},{"Start":"01:00.180 ","End":"01:02.700","Text":"and the R 4."},{"Start":"01:02.700 ","End":"01:05.280","Text":"Remember glycine which is the exception,"},{"Start":"01:05.280 ","End":"01:08.570","Text":"where the I is H. Just look at another 1."},{"Start":"01:08.570 ","End":"01:15.240","Text":"You have the Alpha-carbon and then you have the COO, 1,"},{"Start":"01:15.240 ","End":"01:18.390","Text":"the hydrogen, 2, the amine,"},{"Start":"01:18.390 ","End":"01:21.405","Text":"3, and the R group,"},{"Start":"01:21.405 ","End":"01:25.420","Text":"4, and so on and so forth."}],"ID":28494},{"Watched":false,"Name":"Amino Acid Classification","Duration":"8m 45s","ChapterTopicVideoID":27382,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:01.695","Text":"Hi there. In this section,"},{"Start":"00:01.695 ","End":"00:04.500","Text":"we\u0027re going to talk about amino acid classification"},{"Start":"00:04.500 ","End":"00:06.720","Text":"as part of our main topic of amino acids."},{"Start":"00:06.720 ","End":"00:07.800","Text":"By the end of this section,"},{"Start":"00:07.800 ","End":"00:10.560","Text":"you\u0027ll be able to understand the classification of"},{"Start":"00:10.560 ","End":"00:14.535","Text":"amino acids and the groups of which amino acids are classified into."},{"Start":"00:14.535 ","End":"00:18.135","Text":"Amino acids can be classified by the R group."},{"Start":"00:18.135 ","End":"00:22.875","Text":"We had mentioned that the R group is different between each amino acid."},{"Start":"00:22.875 ","End":"00:24.600","Text":"Knowledge of the chemical properties of"},{"Start":"00:24.600 ","End":"00:28.020","Text":"common amino acids is central to an understanding of biochemistry."},{"Start":"00:28.020 ","End":"00:31.380","Text":"The topic can be simplified by grouping the amino acids into"},{"Start":"00:31.380 ","End":"00:35.025","Text":"5 main groups based on the properties of their R groups."},{"Start":"00:35.025 ","End":"00:39.120","Text":"In particular their polarity or tendency to interact with"},{"Start":"00:39.120 ","End":"00:43.995","Text":"water at biological pH, near pH 7."},{"Start":"00:43.995 ","End":"00:49.370","Text":"The polarity of the R groups varies widely from nonpolar and hydrophobic water"},{"Start":"00:49.370 ","End":"00:56.585","Text":"insoluble to highly polar and hydrophilic, water-soluble."},{"Start":"00:56.585 ","End":"00:59.540","Text":"A few amino acids are somewhat difficult to"},{"Start":"00:59.540 ","End":"01:03.500","Text":"characterize or do not fit perfectly in any group,"},{"Start":"01:03.500 ","End":"01:08.345","Text":"particularly glycine, histidine, and cysteine."},{"Start":"01:08.345 ","End":"01:11.510","Text":"Their assignments to particular groupings are the results of"},{"Start":"01:11.510 ","End":"01:15.325","Text":"considered judgments rather than absolutes."},{"Start":"01:15.325 ","End":"01:21.545","Text":"The structures of the 20 amino acids are shown in the figure with their classifications."},{"Start":"01:21.545 ","End":"01:24.815","Text":"Within each class, there are gradations of polarity,"},{"Start":"01:24.815 ","End":"01:27.725","Text":"size, and shape of the R groups."},{"Start":"01:27.725 ","End":"01:34.850","Text":"We have the R groups in this class of amino acids are nonpolar and hydrophobic."},{"Start":"01:34.850 ","End":"01:37.970","Text":"The side chain of alanine, valine, leucine,"},{"Start":"01:37.970 ","End":"01:41.945","Text":"and isoleucine tend to cluster together within proteins,"},{"Start":"01:41.945 ","End":"01:45.995","Text":"stabilizing protein structure by means of hydrophobic interactions."},{"Start":"01:45.995 ","End":"01:47.860","Text":"Glycine has the simplest structure."},{"Start":"01:47.860 ","End":"01:49.639","Text":"It is formally nonpolar."},{"Start":"01:49.639 ","End":"01:51.200","Text":"It\u0027s very small side chain mixed,"},{"Start":"01:51.200 ","End":"01:53.857","Text":"no real contribution to hydrophobic interactions"},{"Start":"01:53.857 ","End":"01:57.685","Text":"and the side chain is this H chain if you remember."},{"Start":"01:57.685 ","End":"02:00.650","Text":"We mentioned it being the exception of that instead of an R group,"},{"Start":"02:00.650 ","End":"02:01.940","Text":"it has a hydrogen."},{"Start":"02:01.940 ","End":"02:06.560","Text":"Methionine, one of the 2 sulfur containing amino acids has"},{"Start":"02:06.560 ","End":"02:11.315","Text":"a nonpolar thioether group in its side chain."},{"Start":"02:11.315 ","End":"02:14.525","Text":"So we have methionine,"},{"Start":"02:14.525 ","End":"02:18.745","Text":"and this is the nonpolar thioether group."},{"Start":"02:18.745 ","End":"02:24.470","Text":"Proline has an aliphatic side chain with a distinctive cyclic structure."},{"Start":"02:24.470 ","End":"02:28.535","Text":"You see this circular cyclic ring structure,"},{"Start":"02:28.535 ","End":"02:33.200","Text":"the secondary amino group of proline residues is held in"},{"Start":"02:33.200 ","End":"02:35.120","Text":"a rigid confirmation that reduces"},{"Start":"02:35.120 ","End":"02:39.395","Text":"the structural flexibility of polypeptide regions containing protein."},{"Start":"02:39.395 ","End":"02:41.435","Text":"Now just to clarify,"},{"Start":"02:41.435 ","End":"02:45.815","Text":"an aliphatic amino acid is nonpolar and hydrophobic."},{"Start":"02:45.815 ","End":"02:48.200","Text":"Hydrophobicity increases as the number of"},{"Start":"02:48.200 ","End":"02:51.170","Text":"carbon atoms on the hydrocarbon chain increases."},{"Start":"02:51.170 ","End":"02:55.685","Text":"The first group has these 7 amino acids,"},{"Start":"02:55.685 ","End":"03:02.885","Text":"and now we go to the second group that has 3 amino acids and it is aromatic R groups."},{"Start":"03:02.885 ","End":"03:06.765","Text":"Aromatic means this ring."},{"Start":"03:06.765 ","End":"03:12.590","Text":"Phenylalanine, tyrosine, and tryptophan with their aromatic side chains,"},{"Start":"03:12.590 ","End":"03:14.690","Text":"this ring here,"},{"Start":"03:14.690 ","End":"03:19.160","Text":"are relatively nonpolar hydrophobic."},{"Start":"03:19.160 ","End":"03:22.805","Text":"All can participate in hydrophobic interactions."},{"Start":"03:22.805 ","End":"03:27.170","Text":"The hydroxyl group of tyrosine can"},{"Start":"03:27.170 ","End":"03:31.414","Text":"form hydrogen bonds and it is an important functional group in some enzymes,"},{"Start":"03:31.414 ","End":"03:36.290","Text":"tyrosine and tryptophan are significantly more polar than"},{"Start":"03:36.290 ","End":"03:38.765","Text":"phenylalanine because of the tyrosine"},{"Start":"03:38.765 ","End":"03:43.180","Text":"hydroxyl group and the nitrogen of the tryptophan, indole ring."},{"Start":"03:43.180 ","End":"03:47.060","Text":"Tryptophan and tyrosine, and to a much lesser extent,"},{"Start":"03:47.060 ","End":"03:50.975","Text":"phenylalanine, absorb ultraviolet light."},{"Start":"03:50.975 ","End":"03:54.260","Text":"This accounts for the characteristics strong absorbance of light by"},{"Start":"03:54.260 ","End":"03:57.770","Text":"most proteins at a wavelength of 280 nanometers,"},{"Start":"03:57.770 ","End":"04:02.825","Text":"a property exploited by researchers in the characterization of proteins."},{"Start":"04:02.825 ","End":"04:05.735","Text":"Now, these are the 2 groups we just covered."},{"Start":"04:05.735 ","End":"04:07.550","Text":"We said there are 5 in total."},{"Start":"04:07.550 ","End":"04:09.350","Text":"So let\u0027s move on to the third,"},{"Start":"04:09.350 ","End":"04:12.275","Text":"which is the polar uncharged R groups."},{"Start":"04:12.275 ","End":"04:16.070","Text":"The R groups of these amino acids are more soluble in water"},{"Start":"04:16.070 ","End":"04:21.650","Text":"or more hydrophilic than those of the nonpolar amino acids."},{"Start":"04:21.650 ","End":"04:29.315","Text":"Remember, hydrophilic means likes water, associate with water."},{"Start":"04:29.315 ","End":"04:33.380","Text":"Now this is the case because these"},{"Start":"04:33.380 ","End":"04:37.655","Text":"contain functional groups that form hydrogen bonds with water."},{"Start":"04:37.655 ","End":"04:42.395","Text":"This class of amino acids includes threonine,"},{"Start":"04:42.395 ","End":"04:45.275","Text":"cysteine, asparagine, and glutamine."},{"Start":"04:45.275 ","End":"04:49.790","Text":"The polarity of cysteine and threonine is contributed by their hydroxyl groups."},{"Start":"04:49.790 ","End":"04:54.115","Text":"If we look at serine and threonine"},{"Start":"04:54.115 ","End":"05:00.125","Text":"they are hydroxyl groups that contribute to the polarity."},{"Start":"05:00.125 ","End":"05:01.615","Text":"That of cysteine,"},{"Start":"05:01.615 ","End":"05:06.465","Text":"is by its sulfhydryl group"},{"Start":"05:06.465 ","End":"05:10.415","Text":"and that of asparagine and glutamine are by their amide groups."},{"Start":"05:10.415 ","End":"05:15.290","Text":"Asparagine and glutamine are the amides of 2 other amino acids also found in proteins,"},{"Start":"05:15.290 ","End":"05:18.035","Text":"aspartate and glutamate, respectively,"},{"Start":"05:18.035 ","End":"05:22.430","Text":"to which asparagine and glutamine are easily hydrolyzed by acid or base."},{"Start":"05:22.430 ","End":"05:26.045","Text":"Cysteine as readily oxidized to form a covalent linked"},{"Start":"05:26.045 ","End":"05:31.355","Text":"dimeric amino acid called cysteine,"},{"Start":"05:31.355 ","End":"05:36.800","Text":"in which 2 cysteine molecules or residues are joined by disulfide bond."},{"Start":"05:36.800 ","End":"05:41.485","Text":"The disulfide linked residues are strongly hydrophobic nonpolar."},{"Start":"05:41.485 ","End":"05:44.205","Text":"We covered 3 groups thus far."},{"Start":"05:44.205 ","End":"05:45.830","Text":"With the third group,"},{"Start":"05:45.830 ","End":"05:48.695","Text":"we have these 5 amino acids."},{"Start":"05:48.695 ","End":"05:51.610","Text":"We just mentioned there\u0027s a sulfide bond for cysteine."},{"Start":"05:51.610 ","End":"05:56.840","Text":"The disulfide bond plays a special role in the structures of many proteins by"},{"Start":"05:56.840 ","End":"05:59.000","Text":"forming covalent links between parts of"},{"Start":"05:59.000 ","End":"06:02.555","Text":"a protein molecule or between 2 different polypeptide chains."},{"Start":"06:02.555 ","End":"06:06.080","Text":"What you see here is this disulfide bond."},{"Start":"06:06.080 ","End":"06:08.225","Text":"So you have a cysteine,"},{"Start":"06:08.225 ","End":"06:10.370","Text":"you have the SH,"},{"Start":"06:10.370 ","End":"06:14.015","Text":"and then through a process, a reaction,"},{"Start":"06:14.015 ","End":"06:17.150","Text":"you have the hydrogen being removed,"},{"Start":"06:17.150 ","End":"06:20.870","Text":"the proton and now due to this loss,"},{"Start":"06:20.870 ","End":"06:24.955","Text":"these can form a bond and this is our disulfide bond."},{"Start":"06:24.955 ","End":"06:29.900","Text":"Basically, what you see here is a reversible formation"},{"Start":"06:29.900 ","End":"06:35.465","Text":"of a disulfide bond by the oxidation of 2 molecules of cysteine."},{"Start":"06:35.465 ","End":"06:38.830","Text":"You result in a disulfide bond between"},{"Start":"06:38.830 ","End":"06:44.375","Text":"cis residues that stabilize the structure of many proteins."},{"Start":"06:44.375 ","End":"06:46.055","Text":"To the fourth group,"},{"Start":"06:46.055 ","End":"06:50.060","Text":"which is positively charged, basic R groups."},{"Start":"06:50.060 ","End":"06:56.950","Text":"The most hydrophilic R-groups are those that are either positively or negatively charged."},{"Start":"06:56.950 ","End":"07:04.445","Text":"Amino acids in which the R groups have significant positive charge at pH 7 are lysine,"},{"Start":"07:04.445 ","End":"07:10.354","Text":"which has a second primary amino group at the epsilon position on its aliphatic chain."},{"Start":"07:10.354 ","End":"07:15.665","Text":"Lysine has another amino group."},{"Start":"07:15.665 ","End":"07:18.275","Text":"Then you have arginine,"},{"Start":"07:18.275 ","End":"07:20.975","Text":"which has a positively-charged guanidine group, of course,"},{"Start":"07:20.975 ","End":"07:22.685","Text":"you see here,"},{"Start":"07:22.685 ","End":"07:26.735","Text":"and histidine, which has an imidazole group."},{"Start":"07:26.735 ","End":"07:28.475","Text":"This big complex thing."},{"Start":"07:28.475 ","End":"07:31.025","Text":"Histidine, which has an imidazole group."},{"Start":"07:31.025 ","End":"07:32.390","Text":"This complex thing here."},{"Start":"07:32.390 ","End":"07:35.660","Text":"Histidine is the only common amino acid having"},{"Start":"07:35.660 ","End":"07:39.935","Text":"an ionizable side chain with a pKa near neutrality."},{"Start":"07:39.935 ","End":"07:42.470","Text":"In many enzyme catalyzed reactions,"},{"Start":"07:42.470 ","End":"07:49.600","Text":"at least residue facilitates the reaction by serving as a proton donor or acceptor."},{"Start":"07:49.600 ","End":"07:53.980","Text":"Here are the 4 groups we talked about thus far,"},{"Start":"07:53.980 ","End":"07:56.515","Text":"and we\u0027re going into the fifth and last group,"},{"Start":"07:56.515 ","End":"08:00.925","Text":"as mentioned, negatively charged acidic R groups."},{"Start":"08:00.925 ","End":"08:05.230","Text":"The 2 amino acids having R groups with"},{"Start":"08:05.230 ","End":"08:10.690","Text":"a net negative charge at pH 7 are aspartate and glutamate,"},{"Start":"08:10.690 ","End":"08:14.515","Text":"each of which has a second carboxyl group."},{"Start":"08:14.515 ","End":"08:16.045","Text":"You see these here."},{"Start":"08:16.045 ","End":"08:19.705","Text":"This is the second carboxyl group."},{"Start":"08:19.705 ","End":"08:23.995","Text":"Here are the 5 groups that we mentioned, nonpolar aliphatic groups,"},{"Start":"08:23.995 ","End":"08:27.685","Text":"aromatic R groups, polar uncharged R groups,"},{"Start":"08:27.685 ","End":"08:29.740","Text":"positively charged R groups,"},{"Start":"08:29.740 ","End":"08:31.825","Text":"and negatively charged R groups."},{"Start":"08:31.825 ","End":"08:33.635","Text":"Again, as you see here,"},{"Start":"08:33.635 ","End":"08:37.070","Text":"now that we\u0027ve completed the amino acid classification section,"},{"Start":"08:37.070 ","End":"08:40.250","Text":"you should be able to understand the classification of"},{"Start":"08:40.250 ","End":"08:45.180","Text":"amino acids and the groups to which amino acids are classified into."}],"ID":28495},{"Watched":false,"Name":"Exercise 8","Duration":"45s","ChapterTopicVideoID":27383,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.960","Text":"Hi there. Let\u0027s review amino acid classification."},{"Start":"00:03.960 ","End":"00:06.990","Text":"What are amino acids mainly classified by?"},{"Start":"00:06.990 ","End":"00:10.785","Text":"Amino acids can be classified by their side chains, their R group."},{"Start":"00:10.785 ","End":"00:14.535","Text":"The classification is based on the properties of the R groups."},{"Start":"00:14.535 ","End":"00:19.680","Text":"In particular their polarity or tendency to interact with water at biological pH,"},{"Start":"00:19.680 ","End":"00:22.080","Text":"which means near pH 7."},{"Start":"00:22.080 ","End":"00:26.850","Text":"The polarity of the R groups varies widely from non-polar and hydrophobic,"},{"Start":"00:26.850 ","End":"00:32.965","Text":"which means water-insoluble to highly polar and hydrophilic, which means water-soluble."},{"Start":"00:32.965 ","End":"00:37.235","Text":"These characteristics are used to group amino acids together,"},{"Start":"00:37.235 ","End":"00:41.585","Text":"polarity and their ability to interact,"},{"Start":"00:41.585 ","End":"00:45.000","Text":"and how they interact with water."}],"ID":28496},{"Watched":false,"Name":"Exercise 9","Duration":"1m 47s","ChapterTopicVideoID":27371,"CourseChapterTopicPlaylistID":272566,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.900","Text":"Hi there. Welcome to an exercise covering amino acid classification."},{"Start":"00:03.900 ","End":"00:05.760","Text":"How many classes of amino acids are"},{"Start":"00:05.760 ","End":"00:09.585","Text":"the common 20 amino acids grouped into? State what they are."},{"Start":"00:09.585 ","End":"00:11.680","Text":"The amino acids are assigned to 1 of"},{"Start":"00:11.680 ","End":"00:14.865","Text":"the 5 main classes based on the properties of their R groups."},{"Start":"00:14.865 ","End":"00:18.045","Text":"The groups are: 1, non-polar,"},{"Start":"00:18.045 ","End":"00:20.775","Text":"aliphatic R groups, 2,"},{"Start":"00:20.775 ","End":"00:25.065","Text":"an aromatic, remember means to the aromatic rings that they have,"},{"Start":"00:25.065 ","End":"00:30.030","Text":"this cyclic ring-like structure of the R group,"},{"Start":"00:30.030 ","End":"00:33.630","Text":"3, polar uncharged R groups,"},{"Start":"00:33.630 ","End":"00:39.465","Text":"4, positively charged basic R groups,"},{"Start":"00:39.465 ","End":"00:43.895","Text":"5, negatively charged acidic R groups."},{"Start":"00:43.895 ","End":"00:48.785","Text":"You have nonpolar, you have aromatic,"},{"Start":"00:48.785 ","End":"00:50.900","Text":"you have polar uncharged,"},{"Start":"00:50.900 ","End":"00:53.915","Text":"and then you have the positively charged and the negatively charged"},{"Start":"00:53.915 ","End":"00:57.650","Text":"with classify into basic and acidic."},{"Start":"00:57.650 ","End":"00:59.450","Text":"Here are the 5,"},{"Start":"00:59.450 ","End":"01:01.840","Text":"starting with 1,"},{"Start":"01:01.840 ","End":"01:05.595","Text":"non-polar aliphatic R groups,"},{"Start":"01:05.595 ","End":"01:07.470","Text":"and you have the 7."},{"Start":"01:07.470 ","End":"01:11.225","Text":"Next you have the aromatic R groups."},{"Start":"01:11.225 ","End":"01:14.810","Text":"Again, this means this shape,"},{"Start":"01:14.810 ","End":"01:18.785","Text":"the aromatic ring, and that has 3."},{"Start":"01:18.785 ","End":"01:22.940","Text":"Then you have the polar uncharged R groups,"},{"Start":"01:22.940 ","End":"01:24.620","Text":"which you have 5 of,"},{"Start":"01:24.620 ","End":"01:28.205","Text":"and then you have a positively charged R groups."},{"Start":"01:28.205 ","End":"01:31.335","Text":"These are considered basic."},{"Start":"01:31.335 ","End":"01:32.765","Text":"Last but not least,"},{"Start":"01:32.765 ","End":"01:36.965","Text":"you have the negatively charged R groups."},{"Start":"01:36.965 ","End":"01:41.645","Text":"There you have it again, nonpolar aromatic,"},{"Start":"01:41.645 ","End":"01:47.650","Text":"polar, positively charged, and negatively charged."}],"ID":28497}],"Thumbnail":null,"ID":272566},{"Name":"Peptides and Proteins","TopicPlaylistFirstVideoID":0,"Duration":null,"Videos":[{"Watched":false,"Name":"Amino Acid Chains","Duration":"5m 58s","ChapterTopicVideoID":28157,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":"https://www.proprep.uk/Images/Videos_Thumbnails/28157.jpeg","UploadDate":"2021-12-23T19:31:31.3430000","DurationForVideoObject":"PT5M58S","Description":null,"MetaTitle":"Amino Acid Chains: Video + Workbook | Proprep","MetaDescription":"Amino Acids, Peptides, and Proteins - Peptides and Proteins. 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/amino-acids%2c-peptides%2c-and-proteins/peptides-and-proteins/vid29393","VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.510","Text":"Hi, there. We are talking about amino acids, peptides,"},{"Start":"00:03.510 ","End":"00:07.455","Text":"and proteins, and specifically in the section amino acid chains."},{"Start":"00:07.455 ","End":"00:11.505","Text":"By the end of the section, you should be able to describe and understand peptide bond,"},{"Start":"00:11.505 ","End":"00:15.015","Text":"and peptides, oligopeptides, and polypeptides."},{"Start":"00:15.015 ","End":"00:19.215","Text":"We now turn to polymers of amino acids."},{"Start":"00:19.215 ","End":"00:21.405","Text":"The peptides and proteins."},{"Start":"00:21.405 ","End":"00:26.100","Text":"2 amino acid molecules can be covalently joined through"},{"Start":"00:26.100 ","End":"00:32.340","Text":"a substituted amide linkage termed a peptide bond to yield a dipeptide."},{"Start":"00:32.340 ","End":"00:37.862","Text":"Such a linkage is formed by removal of the elements of water, dehydration,"},{"Start":"00:37.862 ","End":"00:44.440","Text":"from the Alpha carboxyl group of 1 amino acid and the Alpha amino group of another."},{"Start":"00:44.440 ","End":"00:49.940","Text":"We have the Alpha carboxyl group of 1 amino acid right here."},{"Start":"00:49.940 ","End":"00:52.670","Text":"COOH is our carboxyl group,"},{"Start":"00:52.670 ","End":"00:54.395","Text":"and that\u0027s the COOH,"},{"Start":"00:54.395 ","End":"00:56.075","Text":"and the Alpha amino group,"},{"Start":"00:56.075 ","End":"01:00.935","Text":"which is our nitrogen based amide."},{"Start":"01:00.935 ","End":"01:05.735","Text":"Peptide bond formation is an example of a condensation reaction,"},{"Start":"01:05.735 ","End":"01:08.915","Text":"a common class of reactions in living cells."},{"Start":"01:08.915 ","End":"01:17.395","Text":"Multiple amino acids can be joined by peptide bonds to form a peptide chain i.e.,"},{"Start":"01:17.395 ","End":"01:21.695","Text":"3 amino acids can be joined by 2 peptide bonds to form a tripeptide."},{"Start":"01:21.695 ","End":"01:25.804","Text":"Similarly, amino acids can be linked to form tetrapeptides,"},{"Start":"01:25.804 ","End":"01:32.045","Text":"pentapeptides, as can be seen in this figure where it\u0027s a dipeptide."},{"Start":"01:32.045 ","End":"01:34.820","Text":"When a few amino acids are joined in this fashion,"},{"Start":"01:34.820 ","End":"01:37.595","Text":"the structure is called an oligopeptide."},{"Start":"01:37.595 ","End":"01:40.130","Text":"When many amino acids are joined,"},{"Start":"01:40.130 ","End":"01:42.715","Text":"the product is called a polypeptide."},{"Start":"01:42.715 ","End":"01:45.680","Text":"Oligopeptide will be multiple amino acids,"},{"Start":"01:45.680 ","End":"01:48.140","Text":"and when it\u0027s not just multiple,"},{"Start":"01:48.140 ","End":"01:52.895","Text":"rather many, then it\u0027s a polypeptide."},{"Start":"01:52.895 ","End":"01:57.014","Text":"Proteins may have thousands of amino acid residues."},{"Start":"01:57.014 ","End":"02:01.070","Text":"Although the term protein and polypeptide are sometimes used interchangeably,"},{"Start":"02:01.070 ","End":"02:05.810","Text":"molecules referred to as polypeptides typically have molecular weights"},{"Start":"02:05.810 ","End":"02:12.260","Text":"below 10,000 while those called proteins have higher molecular weights."},{"Start":"02:12.260 ","End":"02:16.985","Text":"If we look here, you see a formation of a peptide bond by condensation."},{"Start":"02:16.985 ","End":"02:21.680","Text":"The Alpha amino group of 1 amino acid acts as a nucleophile to displace"},{"Start":"02:21.680 ","End":"02:26.760","Text":"the hydroxyl group of another amino acid forming a peptide bond."},{"Start":"02:26.760 ","End":"02:29.390","Text":"That is what we see here, this shaded region."},{"Start":"02:29.390 ","End":"02:31.640","Text":"Amino groups are good nucleophiles,"},{"Start":"02:31.640 ","End":"02:37.925","Text":"but the hydroxyl group is a poor leaving group and is not readily displaced."},{"Start":"02:37.925 ","End":"02:44.524","Text":"At physiological pH, the reaction shown does not occur to any appreciable extent."},{"Start":"02:44.524 ","End":"02:49.235","Text":"As already mentioned, an amino acid unit and a peptide is often called a residue."},{"Start":"02:49.235 ","End":"02:51.650","Text":"In a peptide, the amino residue at the end with"},{"Start":"02:51.650 ","End":"02:55.610","Text":"the free Alpha amino group is the amino terminal or N terminal residue."},{"Start":"02:55.610 ","End":"02:57.830","Text":"The residue at the other end,"},{"Start":"02:57.830 ","End":"02:59.690","Text":"which has a free carboxyl group,"},{"Start":"02:59.690 ","End":"03:01.265","Text":"is the carboxyl terminal,"},{"Start":"03:01.265 ","End":"03:02.924","Text":"the C terminal residue."},{"Start":"03:02.924 ","End":"03:05.885","Text":"An amino acid sequence of a peptide,"},{"Start":"03:05.885 ","End":"03:09.080","Text":"polypeptide or protein is displayed."},{"Start":"03:09.080 ","End":"03:16.235","Text":"The amino terminal end is placed on the left and the carboxyl terminal on the right."},{"Start":"03:16.235 ","End":"03:21.055","Text":"The sequence is read left to right beginning with the amino terminal end."},{"Start":"03:21.055 ","End":"03:24.710","Text":"What you see here is a pentapeptide,"},{"Start":"03:24.710 ","End":"03:26.240","Text":"1, 2, 3,"},{"Start":"03:26.240 ","End":"03:29.810","Text":"4 peptide bonds and that\u0027s because there are 5 peptides,"},{"Start":"03:29.810 ","End":"03:31.550","Text":"1, 2, 3,"},{"Start":"03:31.550 ","End":"03:34.415","Text":"4, 5, pentapeptide."},{"Start":"03:34.415 ","End":"03:41.840","Text":"This means an allele peptide or polypeptide that has 5 peptides that make it up."},{"Start":"03:41.840 ","End":"03:44.480","Text":"Now, looking at this pentapeptide, again,"},{"Start":"03:44.480 ","End":"03:47.660","Text":"we see the peptide bonds are shaded in purple."},{"Start":"03:47.660 ","End":"03:54.585","Text":"You even see here that 1 amino acid residue has this circular ring."},{"Start":"03:54.585 ","End":"03:59.890","Text":"That\u0027s just to emphasize that the R groups,"},{"Start":"03:59.890 ","End":"04:02.275","Text":"the R side groups of each amino acid,"},{"Start":"04:02.275 ","End":"04:07.690","Text":"is what differentiates them and makes each polypeptide very specific."},{"Start":"04:07.690 ","End":"04:12.490","Text":"Although hydrolysis of a peptide bond is an exogenic reaction,"},{"Start":"04:12.490 ","End":"04:15.790","Text":"it occurs slowly because of its high activation energy."},{"Start":"04:15.790 ","End":"04:20.920","Text":"As a result, the peptide bonds in proteins are quite stable,"},{"Start":"04:20.920 ","End":"04:25.505","Text":"which an average half-life of about 7 years in the most intracellular condition."},{"Start":"04:25.505 ","End":"04:29.605","Text":"Peptides can be distinguished by their ionization behavior."},{"Start":"04:29.605 ","End":"04:32.200","Text":"Peptides contain 1 free Alpha amino group and"},{"Start":"04:32.200 ","End":"04:35.845","Text":"1 free Alpha carboxyl group at opposite ends of the chain."},{"Start":"04:35.845 ","End":"04:39.455","Text":"These groups ionize as they do in the free amino acids."},{"Start":"04:39.455 ","End":"04:42.530","Text":"The Alpha amino and Alpha carboxyl groups are all"},{"Start":"04:42.530 ","End":"04:47.615","Text":"non terminal amino acids that are covalently joined in the peptide bonds,"},{"Start":"04:47.615 ","End":"04:49.610","Text":"which do not ionize and thus,"},{"Start":"04:49.610 ","End":"04:53.795","Text":"do not contribute to the total acid-base behavior of peptides."},{"Start":"04:53.795 ","End":"04:56.780","Text":"The acid-base behavior of a peptide can be predicted from"},{"Start":"04:56.780 ","End":"05:00.380","Text":"its free Alpha amino and Alpha carboxyl groups,"},{"Start":"05:00.380 ","End":"05:04.760","Text":"as well as the nature and number of its ionizable R groups,"},{"Start":"05:04.760 ","End":"05:07.460","Text":"since some R groups can ionize as well, and then a peptide,"},{"Start":"05:07.460 ","End":"05:10.595","Text":"these contribute to the overall acid-base behavior, the molecule."},{"Start":"05:10.595 ","End":"05:12.605","Text":"Like free amino acids,"},{"Start":"05:12.605 ","End":"05:17.050","Text":"peptides have characteristic titration curves and a characteristic pH."},{"Start":"05:17.050 ","End":"05:19.160","Text":"These properties are exploited in some of"},{"Start":"05:19.160 ","End":"05:22.190","Text":"the techniques used to separate peptides and proteins."},{"Start":"05:22.190 ","End":"05:28.970","Text":"Now, what you see here is a tetrapeptide because there\u0027s 4 amino acids."},{"Start":"05:28.970 ","End":"05:32.150","Text":"This time it\u0027s a tetrapeptide."},{"Start":"05:32.150 ","End":"05:34.650","Text":"Tetra means 4."},{"Start":"05:34.650 ","End":"05:36.365","Text":"So in this tetrapeptide,"},{"Start":"05:36.365 ","End":"05:41.285","Text":"what you see is the 1 Alpha amino group here,"},{"Start":"05:41.285 ","End":"05:44.065","Text":"and the 1 Alpha carboxyl group,"},{"Start":"05:44.065 ","End":"05:47.060","Text":"and 2 ionizable R groups."},{"Start":"05:47.060 ","End":"05:52.104","Text":"The groups are ionized at pH 7 and are in this."},{"Start":"05:52.104 ","End":"05:55.970","Text":"So at this point you should know what a peptide bond is and in general,"},{"Start":"05:55.970 ","End":"05:59.520","Text":"what peptides, oligopeptides, and polypeptides are."}],"ID":29393},{"Watched":false,"Name":"Exercise 1","Duration":"49s","ChapterTopicVideoID":28158,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.605","Text":"Hi there. What did we learn within the section of amino acid chains?"},{"Start":"00:04.605 ","End":"00:07.950","Text":"Describe the formation of a peptide bond."},{"Start":"00:07.950 ","End":"00:10.770","Text":"2 amino acid molecules can be covalently joined through"},{"Start":"00:10.770 ","End":"00:15.720","Text":"a substituted amide linkage termed a peptide bond to yield a dipeptide."},{"Start":"00:15.720 ","End":"00:18.570","Text":"Such a linkage is formed by removal of the elements of water,"},{"Start":"00:18.570 ","End":"00:21.305","Text":"dehydration, from the Alpha-carboxyl group,"},{"Start":"00:21.305 ","End":"00:27.210","Text":"which would be here, of 1 amino acid and the Alpha amino group of another."},{"Start":"00:27.210 ","End":"00:32.325","Text":"Multiple amino acids can be joined by peptide bonds to form a peptide chain."},{"Start":"00:32.325 ","End":"00:34.700","Text":"When a few amino acids are joined in this fashion,"},{"Start":"00:34.700 ","End":"00:37.025","Text":"the structure is called an oligopeptide."},{"Start":"00:37.025 ","End":"00:38.870","Text":"When many amino acids are joined,"},{"Start":"00:38.870 ","End":"00:41.020","Text":"the product is called a polypeptide."},{"Start":"00:41.020 ","End":"00:42.680","Text":"They have several amino acids joined,"},{"Start":"00:42.680 ","End":"00:44.120","Text":"that is an oligopeptide,"},{"Start":"00:44.120 ","End":"00:45.365","Text":"but when there are many,"},{"Start":"00:45.365 ","End":"00:49.290","Text":"then it graduates to become a polypeptide."}],"ID":29394},{"Watched":false,"Name":"Exercise 2","Duration":"42s","ChapterTopicVideoID":28159,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.880","Text":"Hi, welcome to an exercise covering amino acid chains."},{"Start":"00:02.880 ","End":"00:07.140","Text":"Though the terms protein and polypeptide are sometimes used interchangeably,"},{"Start":"00:07.140 ","End":"00:09.670","Text":"typically there is a difference between them. What is it?"},{"Start":"00:09.670 ","End":"00:13.140","Text":"Molecules referred to as polypeptides typically have a molecular weight"},{"Start":"00:13.140 ","End":"00:17.160","Text":"below 10,000 while those called proteins have higher molecular weight."},{"Start":"00:17.160 ","End":"00:24.030","Text":"Again, you\u0027re seeing here the reaction of hydration where a water molecule is"},{"Start":"00:24.030 ","End":"00:31.905","Text":"extracted by combining an amino group and the carboxyl group of 2 amino acids,"},{"Start":"00:31.905 ","End":"00:35.955","Text":"water is released and then they are forming a dipeptide,"},{"Start":"00:35.955 ","End":"00:39.330","Text":"a polypeptide, and 1 additional form.,"},{"Start":"00:39.330 ","End":"00:42.240","Text":"you have pentapeptide, etc."}],"ID":29395},{"Watched":false,"Name":"Exercise 3","Duration":"25s","ChapterTopicVideoID":28160,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.840","Text":"Welcome to another exercise covering amino acid chains."},{"Start":"00:03.840 ","End":"00:08.385","Text":"In a peptide, the ends are distinctive from each other, describe this."},{"Start":"00:08.385 ","End":"00:11.340","Text":"In a peptide, the amino acid residue at the end with"},{"Start":"00:11.340 ","End":"00:15.884","Text":"a free Alpha amino group is the amino terminal or N-terminal."},{"Start":"00:15.884 ","End":"00:17.580","Text":"The residue at the other end,"},{"Start":"00:17.580 ","End":"00:24.060","Text":"which has a free carboxyl group is the carboxyl-terminal, the C-terminal residue."}],"ID":29396},{"Watched":false,"Name":"Intro to Peptides","Duration":"4m 35s","ChapterTopicVideoID":28161,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:01.410","Text":"Hi there. In this section,"},{"Start":"00:01.410 ","End":"00:05.610","Text":"we are going to introduce the concept of peptides within the chapter of amino acids,"},{"Start":"00:05.610 ","End":"00:07.095","Text":"peptides, and proteins."},{"Start":"00:07.095 ","End":"00:08.670","Text":"By the end of the section,"},{"Start":"00:08.670 ","End":"00:13.395","Text":"you should understand the variety of biologically active peptides and polypeptides."},{"Start":"00:13.395 ","End":"00:17.535","Text":"Biologically active peptides and polypeptides occur in a vast range of sizes."},{"Start":"00:17.535 ","End":"00:20.280","Text":"No generalizations can be made about the molecular weights of"},{"Start":"00:20.280 ","End":"00:23.925","Text":"biologically active peptides and proteins in relation to their functions,"},{"Start":"00:23.925 ","End":"00:26.430","Text":"naturally occurring peptides range in length from 2"},{"Start":"00:26.430 ","End":"00:29.220","Text":"to many thousands of amino acid residues."},{"Start":"00:29.220 ","End":"00:33.345","Text":"Even the smallest peptides can have biologically important effects."},{"Start":"00:33.345 ","End":"00:37.629","Text":"Many small peptides exert their effect at very low concentrations."},{"Start":"00:37.629 ","End":"00:40.505","Text":"A number of vertebrate hormones are small peptides."},{"Start":"00:40.505 ","End":"00:43.760","Text":"These include, for example, oxytocin,"},{"Start":"00:43.760 ","End":"00:47.585","Text":"which you may have heard of in relation to the attachment hormone,"},{"Start":"00:47.585 ","End":"00:52.015","Text":"for example, during breastfeeding or the love hormone which is released."},{"Start":"00:52.015 ","End":"00:59.120","Text":"This is secreted by the posterior pituitary and stimulates uterine contractions."},{"Start":"00:59.120 ","End":"01:01.425","Text":"Another example is Bradykinin,"},{"Start":"01:01.425 ","End":"01:05.660","Text":"which is made of 9 residues and inhibits inflammation of tissues."},{"Start":"01:05.660 ","End":"01:08.165","Text":"Then there\u0027s thyrotropin-releasing factor,"},{"Start":"01:08.165 ","End":"01:09.800","Text":"which is made of 3 residues,"},{"Start":"01:09.800 ","End":"01:14.885","Text":"which is formed in the hypothalamus and stimulates the release of another hormone,"},{"Start":"01:14.885 ","End":"01:19.125","Text":"thyrotropin from the anterior pituitary gland."},{"Start":"01:19.125 ","End":"01:22.745","Text":"Some extremely toxic mushroom poisons are also small peptides,"},{"Start":"01:22.745 ","End":"01:24.995","Text":"as are many antibiotics."},{"Start":"01:24.995 ","End":"01:28.850","Text":"Slightly larger than these are"},{"Start":"01:28.850 ","End":"01:34.354","Text":"small polypeptides and oligonpeptides such as the pancreatic hormone insulin,"},{"Start":"01:34.354 ","End":"01:37.175","Text":"which contains 2 polypeptide chains,"},{"Start":"01:37.175 ","End":"01:41.150","Text":"1 having 30 amino acid residues and the other 21."},{"Start":"01:41.150 ","End":"01:42.650","Text":"Now, as mentioned earlier,"},{"Start":"01:42.650 ","End":"01:47.555","Text":"polypeptide chain lengths in proteins vary considerably."},{"Start":"01:47.555 ","End":"01:51.155","Text":"Human cytochrome C, for example, in humans,"},{"Start":"01:51.155 ","End":"01:54.770","Text":"has 104 amino acid residues linked in"},{"Start":"01:54.770 ","End":"02:02.155","Text":"a single chain with a molecular weight of 13,000 at the extreme is Titin,"},{"Start":"02:02.155 ","End":"02:05.550","Text":"which is also made of 1 chain,"},{"Start":"02:05.550 ","End":"02:09.799","Text":"that is made of close to nearly 27,000"},{"Start":"02:09.799 ","End":"02:16.570","Text":"amino acid residues and a molecular weight of about 3 million,"},{"Start":"02:16.570 ","End":"02:20.870","Text":"the vast majority of naturally occurring proteins are much"},{"Start":"02:20.870 ","End":"02:25.280","Text":"smaller than this and contain fewer than 2,000 amino acid residues."},{"Start":"02:25.280 ","End":"02:28.850","Text":"Some proteins consist of a single polypeptide chain as seen in"},{"Start":"02:28.850 ","End":"02:34.190","Text":"cytochrome c or the case of serum albumin and humans as well as Titin,"},{"Start":"02:34.190 ","End":"02:35.533","Text":"which we had mentioned,"},{"Start":"02:35.533 ","End":"02:39.120","Text":"and others called multi sub-unit proteins,"},{"Start":"02:39.120 ","End":"02:43.805","Text":"have 2 or more polypeptides associated non-covalently."},{"Start":"02:43.805 ","End":"02:46.460","Text":"The individual polypeptide chains and"},{"Start":"02:46.460 ","End":"02:51.080","Text":"multi sub-unit proteins may be identical or different."},{"Start":"02:51.080 ","End":"02:57.470","Text":"When you\u0027re looking at the multiple sub-unit proteins,"},{"Start":"02:57.470 ","End":"03:02.900","Text":"polypeptide chains, they may be the same or different."},{"Start":"03:02.900 ","End":"03:04.776","Text":"If at least 2 are identical,"},{"Start":"03:04.776 ","End":"03:09.260","Text":"the protein is said to be oligomeric and"},{"Start":"03:09.260 ","End":"03:11.660","Text":"the identical units consisting of"},{"Start":"03:11.660 ","End":"03:16.930","Text":"1 or more polypeptide chains are referred to as protomers."},{"Start":"03:16.930 ","End":"03:19.365","Text":"Hemoglobin, for example,"},{"Start":"03:19.365 ","End":"03:22.095","Text":"has 4 polypeptide sub-units,"},{"Start":"03:22.095 ","End":"03:23.760","Text":"2 identical Alpha chains,"},{"Start":"03:23.760 ","End":"03:25.540","Text":"and 2 identical Beta chains."},{"Start":"03:25.540 ","End":"03:28.105","Text":"When we\u0027re looking at hemoglobin,"},{"Start":"03:28.105 ","End":"03:30.880","Text":"we have 4 polypeptide chains,"},{"Start":"03:30.880 ","End":"03:39.689","Text":"with 2 being identical Alpha chains and 2 being identical Beta chains,"},{"Start":"03:39.689 ","End":"03:46.030","Text":"and all 4 of these are held together by non-covalent interactions."},{"Start":"03:46.030 ","End":"03:49.915","Text":"Each Alpha sub-unit is paired in an identical with"},{"Start":"03:49.915 ","End":"03:54.325","Text":"a Beta sub-unit within the structure of this multi sub-unit protein."},{"Start":"03:54.325 ","End":"03:58.300","Text":"That hemoglobin can be considered either a tetramer of"},{"Start":"03:58.300 ","End":"04:05.065","Text":"4 polypeptides sub-units or a dimer of Alpha-Beta protomers."},{"Start":"04:05.065 ","End":"04:07.095","Text":"Remember our term protomer,"},{"Start":"04:07.095 ","End":"04:13.115","Text":"which is when you have identical units and oligomeric protein."},{"Start":"04:13.115 ","End":"04:17.975","Text":"A few proteins contain 2 or more polypeptide chains linked covalently."},{"Start":"04:17.975 ","End":"04:23.330","Text":"For example, the 2 polypeptide chains of insulin are linked by disulfide bonds."},{"Start":"04:23.330 ","End":"04:26.570","Text":"In such cases, the individual polypeptides are not considered"},{"Start":"04:26.570 ","End":"04:30.200","Text":"sub-units but are commonly referred to simply as chains."},{"Start":"04:30.200 ","End":"04:32.120","Text":"So at this point, when we talked about the variety of"},{"Start":"04:32.120 ","End":"04:35.940","Text":"biologically active peptides and polypeptides."}],"ID":29397},{"Watched":false,"Name":"Exercise 4","Duration":"37s","ChapterTopicVideoID":28162,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:06.120","Text":"We have an exercise for the section where we introduced peptides."},{"Start":"00:06.120 ","End":"00:09.990","Text":"Define the terms oligomeric protein and protomer."},{"Start":"00:09.990 ","End":"00:12.765","Text":"Some proteins consist of a single polypeptide chain."},{"Start":"00:12.765 ","End":"00:15.300","Text":"Others, termed multisubunit proteins,"},{"Start":"00:15.300 ","End":"00:18.570","Text":"have 2 or more polypeptides associated non-covalently."},{"Start":"00:18.570 ","End":"00:20.310","Text":"The individual polypeptide chains in"},{"Start":"00:20.310 ","End":"00:24.329","Text":"a multisubunit protein may be identical or different."},{"Start":"00:24.329 ","End":"00:27.120","Text":"If at least 2 of the polypeptide chains are identical,"},{"Start":"00:27.120 ","End":"00:30.840","Text":"the protein is said to be an oligomeric protein."},{"Start":"00:30.840 ","End":"00:37.780","Text":"The identical polypeptide chain units are referred to as protomers."}],"ID":29398},{"Watched":false,"Name":"Exercise 5","Duration":"2m 18s","ChapterTopicVideoID":28163,"CourseChapterTopicPlaylistID":277599,"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":"Hi there. Welcome to another exercise within this section of intro to peptides."},{"Start":"00:05.010 ","End":"00:07.050","Text":"Which of these statements is false?"},{"Start":"00:07.050 ","End":"00:09.690","Text":"A, naturally occurring peptides range in"},{"Start":"00:09.690 ","End":"00:13.155","Text":"length from 2 to many thousands of amino acid residues."},{"Start":"00:13.155 ","End":"00:17.685","Text":"B, even the smallest peptides can have biologically important effects."},{"Start":"00:17.685 ","End":"00:22.425","Text":"C, many small peptides exert their effect at very low concentrations."},{"Start":"00:22.425 ","End":"00:26.550","Text":"D, some toxic mushroom poisons are also small peptides,"},{"Start":"00:26.550 ","End":"00:28.470","Text":"as are many antibiotics."},{"Start":"00:28.470 ","End":"00:31.470","Text":"E, the vast majority of naturally occurring proteins"},{"Start":"00:31.470 ","End":"00:34.650","Text":"contain more than 2,000 amino acid residues."},{"Start":"00:34.650 ","End":"00:36.910","Text":"Let\u0027s go by this one-by- one."},{"Start":"00:36.910 ","End":"00:39.560","Text":"Naturally occurring peptides range in length from"},{"Start":"00:39.560 ","End":"00:42.430","Text":"2 to many thousands of amino acid residues."},{"Start":"00:42.430 ","End":"00:46.130","Text":"We did mention that they can range from the very"},{"Start":"00:46.130 ","End":"00:50.285","Text":"small 2 to many thousands of amino acid residues."},{"Start":"00:50.285 ","End":"00:52.940","Text":"This is a true statement, therefore,"},{"Start":"00:52.940 ","End":"00:57.675","Text":"it is not correct for our false statement, so we\u0027ll move on to B."},{"Start":"00:57.675 ","End":"01:00.665","Text":"Even the smallest peptides can have biologically important effects."},{"Start":"01:00.665 ","End":"01:02.420","Text":"Well, that is true as well,"},{"Start":"01:02.420 ","End":"01:05.660","Text":"we mentioned hormones, oxytocin, etc.,"},{"Start":"01:05.660 ","End":"01:07.910","Text":"having only 3 amino acid residues and"},{"Start":"01:07.910 ","End":"01:11.530","Text":"these being important and having significant effects."},{"Start":"01:11.530 ","End":"01:13.370","Text":"B, as well,"},{"Start":"01:13.370 ","End":"01:16.235","Text":"is not our answer because it is a true statement."},{"Start":"01:16.235 ","End":"01:20.870","Text":"C, many small peptides exert their effects at very low concentrations."},{"Start":"01:20.870 ","End":"01:25.205","Text":"Well, we specified that and this is very true."},{"Start":"01:25.205 ","End":"01:28.070","Text":"You do not need very high concentrations of"},{"Start":"01:28.070 ","End":"01:32.860","Text":"certain hormones in order for them to exert their effect as an example."},{"Start":"01:32.860 ","End":"01:35.570","Text":"This, again, is a true statement,"},{"Start":"01:35.570 ","End":"01:37.970","Text":"therefore, it is not our answer."},{"Start":"01:37.970 ","End":"01:42.695","Text":"D, some toxic mushroom poisons are also small peptides as are many antibiotics."},{"Start":"01:42.695 ","End":"01:44.645","Text":"Well, we said this word for word."},{"Start":"01:44.645 ","End":"01:47.975","Text":"This is true, therefore it is not our answer."},{"Start":"01:47.975 ","End":"01:49.970","Text":"E, the vast majority of"},{"Start":"01:49.970 ","End":"01:54.650","Text":"naturally occurring proteins contain more than 2,000 amino acid residues."},{"Start":"01:54.650 ","End":"01:57.650","Text":"Well, we said the opposite is true."},{"Start":"01:57.650 ","End":"02:04.910","Text":"Actually, it is the incorrect statement because it is less than 2,000."},{"Start":"02:04.910 ","End":"02:10.025","Text":"Therefore, this is our false statement and our correct answer."},{"Start":"02:10.025 ","End":"02:11.300","Text":"How do we make it correct?"},{"Start":"02:11.300 ","End":"02:14.300","Text":"As mentioned, the vast majority of naturally occurring proteins contain"},{"Start":"02:14.300 ","End":"02:19.290","Text":"fewer than 2,000 amino acid residues."}],"ID":29399},{"Watched":false,"Name":"Exercise 6","Duration":"42s","ChapterTopicVideoID":28164,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.485","Text":"Here we are with another exercise after our section,"},{"Start":"00:04.485 ","End":"00:06.615","Text":"where we introduced peptides."},{"Start":"00:06.615 ","End":"00:10.245","Text":"What are oxytocin and bradykinin examples of?"},{"Start":"00:10.245 ","End":"00:15.615","Text":"These are both examples of vertebrate hormones which are small peptides."},{"Start":"00:15.615 ","End":"00:18.255","Text":"Oxytocin has 9 amino acid residues,"},{"Start":"00:18.255 ","End":"00:24.975","Text":"which is secreted by the posterior pituitary and stimulates uterine contractions."},{"Start":"00:24.975 ","End":"00:30.045","Text":"We also mentioned bradykinin having 9 residues,"},{"Start":"00:30.045 ","End":"00:34.605","Text":"and this hormone is important for inhibition of inflammation of tissues."},{"Start":"00:34.605 ","End":"00:42.010","Text":"Our examples of vertebrate hormones that are very important for our functioning."}],"ID":29400},{"Watched":false,"Name":"Protein Compositions","Duration":"3m 45s","ChapterTopicVideoID":28152,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.110 ","End":"00:03.905","Text":"Hi there. Let\u0027s talk about protein compositions"},{"Start":"00:03.905 ","End":"00:06.870","Text":"within the chapter amino acids, peptides, and proteins."},{"Start":"00:06.870 ","End":"00:10.469","Text":"By the end of this section, you should be able to understand"},{"Start":"00:10.469 ","End":"00:15.195","Text":"the concept of polypeptide composition and calculate amino acid composition."},{"Start":"00:15.195 ","End":"00:18.540","Text":"Polypeptides have characteristic amino acid compositions."},{"Start":"00:18.540 ","End":"00:22.319","Text":"Amino acid composition of proteins is highly variable."},{"Start":"00:22.319 ","End":"00:28.395","Text":"The 20 common amino acids almost never occur in equal amounts in a protein,"},{"Start":"00:28.395 ","End":"00:35.310","Text":"meaning these will all vary in the amounts of each one in a protein."},{"Start":"00:35.310 ","End":"00:41.015","Text":"Hydrolysis of peptides or proteins with acid yields a mixture of free Alpha-amino acids."},{"Start":"00:41.015 ","End":"00:44.960","Text":"When completely hydrolyzed, each type of protein yields"},{"Start":"00:44.960 ","End":"00:49.489","Text":"a characteristic proportion of mixture of the different amino acids."},{"Start":"00:49.489 ","End":"00:52.980","Text":"Some amino acids may occur only once or not at all on"},{"Start":"00:52.980 ","End":"00:57.005","Text":"a given type of protein and others may occur in large numbers."},{"Start":"00:57.005 ","End":"01:00.530","Text":"Complete hydrolysis alone is not sufficient for"},{"Start":"01:00.530 ","End":"01:03.020","Text":"an exact analysis of amino acid composition"},{"Start":"01:03.020 ","End":"01:06.205","Text":"because some side reactions occur during the procedure."},{"Start":"01:06.205 ","End":"01:10.850","Text":"Now, we can calculate the approximate number of amino acid residues in"},{"Start":"01:10.850 ","End":"01:12.470","Text":"a simple protein containing"},{"Start":"01:12.470 ","End":"01:18.530","Text":"no other chemical constituents by dividing its molecular weight by 110."},{"Start":"01:18.530 ","End":"01:24.305","Text":"Although the average molecular weight of the 20 common amino acids is about 138,"},{"Start":"01:24.305 ","End":"01:27.970","Text":"the smaller amino acids predominate in most proteins."},{"Start":"01:27.970 ","End":"01:30.020","Text":"If we take into account the proportions in"},{"Start":"01:30.020 ","End":"01:32.360","Text":"which the various amino acids of current proteins,"},{"Start":"01:32.360 ","End":"01:37.195","Text":"the average molecular weight of protein amino acid is near to 128."},{"Start":"01:37.195 ","End":"01:41.570","Text":"That\u0027s due to the small ones being more prevalent."},{"Start":"01:41.570 ","End":"01:43.700","Text":"If we take into account the operation in which"},{"Start":"01:43.700 ","End":"01:45.800","Text":"the various amino acids occur in proteins,"},{"Start":"01:45.800 ","End":"01:48.955","Text":"the average molecular weight of protein amino acids is near to 120."},{"Start":"01:48.955 ","End":"01:50.420","Text":"A molecule of water,"},{"Start":"01:50.420 ","End":"01:52.640","Text":"as seen here with its molecular weight,"},{"Start":"01:52.640 ","End":"01:55.490","Text":"is removed to create each peptide bond."},{"Start":"01:55.490 ","End":"01:57.695","Text":"Taking that into account,"},{"Start":"01:57.695 ","End":"02:03.440","Text":"the average molecular weight of an amino acid residue in a protein is about 128 minus 18,"},{"Start":"02:03.440 ","End":"02:06.845","Text":"which leaves us with 110."},{"Start":"02:06.845 ","End":"02:10.910","Text":"Some proteins contain chemical groups other than amino acids."},{"Start":"02:10.910 ","End":"02:14.330","Text":"On the other hand, there are proteins that contain only amino acid residues."},{"Start":"02:14.330 ","End":"02:16.910","Text":"These are simple proteins."},{"Start":"02:16.910 ","End":"02:20.660","Text":"They have no other chemical constituents within them."},{"Start":"02:20.660 ","End":"02:23.480","Text":"However, some proteins contain"},{"Start":"02:23.480 ","End":"02:28.715","Text":"permanently associated chemical components in addition to amino acids,"},{"Start":"02:28.715 ","End":"02:32.230","Text":"and these are called conjugated proteins."},{"Start":"02:32.230 ","End":"02:38.135","Text":"The non-amino acid part of a conjugated protein is usually called its prosthetic group."},{"Start":"02:38.135 ","End":"02:40.790","Text":"These conjugated proteins are"},{"Start":"02:40.790 ","End":"02:44.795","Text":"classified on the basis of a chemical nature of their prosthetic."},{"Start":"02:44.795 ","End":"02:46.310","Text":"What does this mean?"},{"Start":"02:46.310 ","End":"02:52.955","Text":"Glycoproteins contain sugar groups and metalloproteins contain a specific metal."},{"Start":"02:52.955 ","End":"02:56.900","Text":"A number of proteins contain more than 1 prosthetic group."},{"Start":"02:56.900 ","End":"02:59.240","Text":"Usually, the prosthetic group plays"},{"Start":"02:59.240 ","End":"03:02.405","Text":"an important role in the protein\u0027s biological function."},{"Start":"03:02.405 ","End":"03:03.590","Text":"Looking at the table here,"},{"Start":"03:03.590 ","End":"03:08.135","Text":"what we see is the different classes of conjugated proteins,"},{"Start":"03:08.135 ","End":"03:12.390","Text":"their prosthetic group, and examples of each one."},{"Start":"03:12.390 ","End":"03:15.740","Text":"If we have a nucleoprotein,"},{"Start":"03:15.740 ","End":"03:20.870","Text":"the prosthetic group is nucleic acids and an example of"},{"Start":"03:20.870 ","End":"03:27.095","Text":"such protein or polyprotein is a virus as you see here."},{"Start":"03:27.095 ","End":"03:31.970","Text":"Furthermore, hemoglobin, this fall within 2 sections."},{"Start":"03:31.970 ","End":"03:35.610","Text":"You have hemoprotein and we have metalloprotein."},{"Start":"03:35.610 ","End":"03:39.600","Text":"With that, we completed the section protein compositions."},{"Start":"03:39.600 ","End":"03:42.080","Text":"We introduced the idea of polypeptide composition"},{"Start":"03:42.080 ","End":"03:46.380","Text":"and calculation of amino acid composition."}],"ID":29388},{"Watched":false,"Name":"Exercise 7","Duration":"2m 38s","ChapterTopicVideoID":28153,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.050","Text":"Now that we\u0027ve introduced the concept of protein compositions,"},{"Start":"00:04.050 ","End":"00:05.985","Text":"let\u0027s dive into an exercise."},{"Start":"00:05.985 ","End":"00:09.210","Text":"Which statement about protein composition is false?"},{"Start":"00:09.210 ","End":"00:13.525","Text":"A, amino acid composition of proteins is highly variable."},{"Start":"00:13.525 ","End":"00:18.990","Text":"B, the 20 common amino acids almost never occur in equal amounts in a protein."},{"Start":"00:18.990 ","End":"00:21.186","Text":"C, when completely hydrolyzed,"},{"Start":"00:21.186 ","End":"00:22.530","Text":"each type of protein yields"},{"Start":"00:22.530 ","End":"00:26.550","Text":"a characteristic proportion or mixture of the different amino acids."},{"Start":"00:26.550 ","End":"00:31.230","Text":"D, we can calculate the approximate number of amino acid residues in a simple protein"},{"Start":"00:31.230 ","End":"00:36.010","Text":"contain no other chemical constituents by dividing its molecular weight by 110."},{"Start":"00:36.010 ","End":"00:41.524","Text":"E, all proteins contain chemical groups other than amino acids."},{"Start":"00:41.524 ","End":"00:46.010","Text":"Starting with A, amino acid composition of proteins is highly variable."},{"Start":"00:46.010 ","End":"00:51.680","Text":"This is how we started the lesson and mentioned it throughout."},{"Start":"00:51.680 ","End":"00:54.450","Text":"This is true, therefore,"},{"Start":"00:54.450 ","End":"00:57.300","Text":"it\u0027s not our desired sentence."},{"Start":"00:57.300 ","End":"01:01.475","Text":"It can\u0027t be the 20 common amino acids almost never occur in equal amounts in protein."},{"Start":"01:01.475 ","End":"01:06.065","Text":"Well, we mentioned how it varies and with a 21 acids,"},{"Start":"01:06.065 ","End":"01:10.955","Text":"you can have it appearing once in a protein or not at all, or few times."},{"Start":"01:10.955 ","End":"01:13.370","Text":"This seems like a true statement, therefore,"},{"Start":"01:13.370 ","End":"01:16.460","Text":"it is not our answer for being false."},{"Start":"01:16.460 ","End":"01:19.820","Text":"We can move to C. When completely hydrolyzed,"},{"Start":"01:19.820 ","End":"01:22.610","Text":"each type of protein yields a characteristic proportion"},{"Start":"01:22.610 ","End":"01:25.895","Text":"or mixture of the different amino acids."},{"Start":"01:25.895 ","End":"01:30.030","Text":"Some amino acids they occur only once or not at all in a given type of protein,"},{"Start":"01:30.030 ","End":"01:33.140","Text":"and others may occur in large numbers."},{"Start":"01:33.140 ","End":"01:36.440","Text":"This, again, is a true statement, therefore,"},{"Start":"01:36.440 ","End":"01:41.220","Text":"it is not the correct answer as being defining as a false statement."},{"Start":"01:41.220 ","End":"01:43.490","Text":"We\u0027re moving on to D,"},{"Start":"01:43.490 ","End":"01:47.570","Text":"we can calculate the approximate number of amino acid residues in a simple protein"},{"Start":"01:47.570 ","End":"01:52.805","Text":"containing no other chemical constituents by dividing its molecular weight by 110."},{"Start":"01:52.805 ","End":"01:56.780","Text":"That is already taking into account a few factors that"},{"Start":"01:56.780 ","End":"02:01.115","Text":"join in and effective and we moved forward from that."},{"Start":"02:01.115 ","End":"02:06.110","Text":"E, all proteins contain chemical groups other than amino acids."},{"Start":"02:06.110 ","End":"02:09.860","Text":"Well, this seems like it\u0027s a false statement because we know there are"},{"Start":"02:09.860 ","End":"02:14.914","Text":"some proteins that are only made of amino acids,"},{"Start":"02:14.914 ","End":"02:23.585","Text":"while some do have a chemical group which is referred to as a prosthetic group."},{"Start":"02:23.585 ","End":"02:28.280","Text":"E sounds like it is our correct answer because it is false."},{"Start":"02:28.280 ","End":"02:30.770","Text":"In order to make it true,"},{"Start":"02:30.770 ","End":"02:38.160","Text":"we would have to say only some proteins contain chemical groups other than amino acids."}],"ID":29389},{"Watched":false,"Name":"Exercise 8","Duration":"46s","ChapterTopicVideoID":28154,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.025","Text":"Hi there. We are exercising our knowledge on protein compositions."},{"Start":"00:05.025 ","End":"00:10.500","Text":"Part 1 to find conjugated proteins and how it is different from a simple protein."},{"Start":"00:10.500 ","End":"00:14.490","Text":"Some proteins contain chemical groups other than amino acids."},{"Start":"00:14.490 ","End":"00:17.895","Text":"In this context, proteins that contain"},{"Start":"00:17.895 ","End":"00:20.580","Text":"only amino acid residues and"},{"Start":"00:20.580 ","End":"00:24.600","Text":"no other chemical constituents are considered simple proteins."},{"Start":"00:24.600 ","End":"00:28.320","Text":"But proteins that contain permanently associated chemical components in"},{"Start":"00:28.320 ","End":"00:32.685","Text":"addition to the amino acids are called conjugated proteins."},{"Start":"00:32.685 ","End":"00:37.920","Text":"Part 2, what is the non amino acid part of a conjugated protein called?"},{"Start":"00:37.920 ","End":"00:40.335","Text":"The number of proteins contain more than 1 prosthetic group."},{"Start":"00:40.335 ","End":"00:41.820","Text":"Usually the prosthetic group plays"},{"Start":"00:41.820 ","End":"00:46.200","Text":"an important role in the protein\u0027s biological function."}],"ID":29390},{"Watched":false,"Name":"Exercise 9","Duration":"1m 4s","ChapterTopicVideoID":28155,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:03.060","Text":"Let\u0027s go through another exercise on putting compositions."},{"Start":"00:03.060 ","End":"00:06.345","Text":"How are conjugated proteins, classified?"},{"Start":"00:06.345 ","End":"00:08.610","Text":"Conjugated proteins are classified on the basis"},{"Start":"00:08.610 ","End":"00:11.595","Text":"of the chemical nature of their prosthetic group."},{"Start":"00:11.595 ","End":"00:16.335","Text":"For example, as you see here is the class of the conjugated protein,"},{"Start":"00:16.335 ","End":"00:18.090","Text":"and the actual prosthetic group,"},{"Start":"00:18.090 ","End":"00:21.345","Text":"and some examples of these, for example,"},{"Start":"00:21.345 ","End":"00:26.600","Text":"lipoproteins contain lipids as you could see here."},{"Start":"00:26.600 ","End":"00:30.560","Text":"Glycoprotein, like glycogen, contain"},{"Start":"00:30.560 ","End":"00:36.530","Text":"sugar groups while metalloproteins contain a specific metal."},{"Start":"00:36.530 ","End":"00:38.230","Text":"Just expand on this a little more,"},{"Start":"00:38.230 ","End":"00:41.675","Text":"a number of proteins containing more than 1 prosthetic group."},{"Start":"00:41.675 ","End":"00:43.250","Text":"Usually, the prosthetic group plays"},{"Start":"00:43.250 ","End":"00:46.750","Text":"an important role in the protein\u0027s biological function."},{"Start":"00:46.750 ","End":"00:48.440","Text":"If we look here,"},{"Start":"00:48.440 ","End":"00:52.100","Text":"we have hemoglobin as an example of hemoprotein,"},{"Start":"00:52.100 ","End":"00:53.890","Text":"haem, blood,"},{"Start":"00:53.890 ","End":"00:57.710","Text":"and metalloprotein, in this case it\u0027s the iron and zinc."},{"Start":"00:57.710 ","End":"01:00.260","Text":"Most of the iron that allows for the association"},{"Start":"01:00.260 ","End":"01:03.840","Text":"with oxygen and carrying it throughout the body where it\u0027s needed."}],"ID":29391},{"Watched":false,"Name":"Exercise 10","Duration":"1m 55s","ChapterTopicVideoID":28156,"CourseChapterTopicPlaylistID":277599,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:01.070 ","End":"00:06.300","Text":"We\u0027re within protein composition and we have another exercise."},{"Start":"00:06.300 ","End":"00:08.235","Text":"Complete the sentences."},{"Start":"00:08.235 ","End":"00:10.545","Text":"A, blank,"},{"Start":"00:10.545 ","End":"00:13.005","Text":"proteins only contain amino acid residues,"},{"Start":"00:13.005 ","End":"00:15.570","Text":"but not other chemical components."},{"Start":"00:15.570 ","End":"00:18.630","Text":"Blank, proteins contain amino acid residues and"},{"Start":"00:18.630 ","End":"00:23.475","Text":"other permanently associated chemical components."},{"Start":"00:23.475 ","End":"00:27.555","Text":"Prosthetic group, bound,"},{"Start":"00:27.555 ","End":"00:31.780","Text":"amino acid parts of a conjugated protein."},{"Start":"00:31.910 ","End":"00:36.720","Text":"Throughout here by the fact that I\u0027m introducing all 3 sentences at once."},{"Start":"00:36.720 ","End":"00:39.885","Text":"We\u0027re getting clues as to what the answers would be."},{"Start":"00:39.885 ","End":"00:42.710","Text":"The answer to that would be simple proteins."},{"Start":"00:42.710 ","End":"00:44.750","Text":"Simple proteins are ones that only contain"},{"Start":"00:44.750 ","End":"00:47.555","Text":"amino acid residues but no other chemical components."},{"Start":"00:47.555 ","End":"00:49.820","Text":"Next, what proteins contain"},{"Start":"00:49.820 ","End":"00:53.690","Text":"amino acid residues and other permanently associated chemical components?"},{"Start":"00:53.690 ","End":"01:01.055","Text":"Well, these have something combined and we introduce the term conjugated proteins."},{"Start":"01:01.055 ","End":"01:04.070","Text":"Conjugated proteins are ones that contain amino acid residues and"},{"Start":"01:04.070 ","End":"01:07.270","Text":"other permanently associated chemical components."},{"Start":"01:07.270 ","End":"01:08.735","Text":"We gave some examples."},{"Start":"01:08.735 ","End":"01:10.055","Text":"I will not mention them."},{"Start":"01:10.055 ","End":"01:12.890","Text":"I\u0027ll let you try to wreck your brain for these."},{"Start":"01:12.890 ","End":"01:21.935","Text":"If need be, go back to the lecture to see examples and following suit."},{"Start":"01:21.935 ","End":"01:25.085","Text":"Next, we have the prosthetic group."},{"Start":"01:25.085 ","End":"01:26.630","Text":"What is this?"},{"Start":"01:26.630 ","End":"01:29.794","Text":"Well, this is something bound,"},{"Start":"01:29.794 ","End":"01:33.630","Text":"something amino acid parts of a conjugated protein."},{"Start":"01:34.780 ","End":"01:39.470","Text":"A prosthetic group is something in the conjugated protein."},{"Start":"01:39.470 ","End":"01:46.010","Text":"We mentioned that there\u0027s something that\u0027s associated in this conjugated proteins."},{"Start":"01:46.010 ","End":"01:49.100","Text":"We can say the prosthetic group is tightly"},{"Start":"01:49.100 ","End":"01:54.570","Text":"bound non-amino acid part of a conjugated protein."}],"ID":29392}],"Thumbnail":null,"ID":277599},{"Name":"Sequence and Proteins","TopicPlaylistFirstVideoID":0,"Duration":null,"Videos":[{"Watched":false,"Name":"Sequence and Protein Function","Duration":"10m 42s","ChapterTopicVideoID":28174,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.140 ","End":"00:05.510","Text":"Hey there, we\u0027re within the chapter of amino acids, peptides and proteins."},{"Start":"00:05.510 ","End":"00:08.415","Text":"In this topic within sequence in proteins,"},{"Start":"00:08.415 ","End":"00:11.985","Text":"we were actually going to talk about sequence and protein function."},{"Start":"00:11.985 ","End":"00:14.700","Text":"By the end of the section, you should be able to talk about"},{"Start":"00:14.700 ","End":"00:18.285","Text":"the characteristics of a protein sequence and amino acid sequence."},{"Start":"00:18.285 ","End":"00:22.110","Text":"The link between the genetic sequence and protein sequence,"},{"Start":"00:22.110 ","End":"00:25.095","Text":"and the link between the protein sequence and function."},{"Start":"00:25.095 ","End":"00:27.315","Text":"As mentioned in the previous lesson,"},{"Start":"00:27.315 ","End":"00:33.105","Text":"the amino acid sequence of a protein determines its function."},{"Start":"00:33.105 ","End":"00:34.365","Text":"Now in this section,"},{"Start":"00:34.365 ","End":"00:38.250","Text":"we are going to talk about how these are related,"},{"Start":"00:38.250 ","End":"00:42.170","Text":"the actual sequence and the function."},{"Start":"00:42.170 ","End":"00:43.250","Text":"Each type of protein has"},{"Start":"00:43.250 ","End":"00:47.105","Text":"a unique amino acid sequence that confers a 3-dimensional structure."},{"Start":"00:47.105 ","End":"00:51.260","Text":"You can see here, there is the amino acid sequence lysine,"},{"Start":"00:51.260 ","End":"00:52.610","Text":"lysine, glycine, glycine, leucine,"},{"Start":"00:52.610 ","End":"00:54.910","Text":"valine, alanine, histidine, et cetera."},{"Start":"00:54.910 ","End":"00:59.270","Text":"This structure confers the protein function."},{"Start":"00:59.270 ","End":"01:01.460","Text":"Now we will go into further detail,"},{"Start":"01:01.460 ","End":"01:07.925","Text":"but you have the 4 layers of the actual structure of the protein."},{"Start":"01:07.925 ","End":"01:11.480","Text":"These are all affected in this 3-dimensional structures"},{"Start":"01:11.480 ","End":"01:15.650","Text":"affected by the actual amino acid sequence,"},{"Start":"01:15.650 ","End":"01:17.780","Text":"which is considered the primary structure."},{"Start":"01:17.780 ","End":"01:21.055","Text":"Let\u0027s go into an example: Eschericia Coli, E. coli,"},{"Start":"01:21.055 ","End":"01:25.760","Text":"this bacterium, produces more than 3,000 different proteins."},{"Start":"01:25.760 ","End":"01:28.820","Text":"If you look at a prokaryotic mRNA,"},{"Start":"01:28.820 ","End":"01:31.295","Text":"because we know E. coli is a bacteria,"},{"Start":"01:31.295 ","End":"01:33.434","Text":"which means it\u0027s a prokaryote,"},{"Start":"01:33.434 ","End":"01:35.615","Text":"therefore, it\u0027s mRNA,"},{"Start":"01:35.615 ","End":"01:40.280","Text":"messenger RNA that encodes for proteins based on"},{"Start":"01:40.280 ","End":"01:47.419","Text":"the genetic code is what give the directions and codes for these proteins."},{"Start":"01:47.419 ","End":"01:55.190","Text":"What you see in prokaryotic mRNA is a sequence with multiple translation starts sites,"},{"Start":"01:55.190 ","End":"02:00.750","Text":"multiple sites where a ribosome will read the sequence,"},{"Start":"02:00.750 ","End":"02:03.695","Text":"and turn it into a protein."},{"Start":"02:03.695 ","End":"02:06.710","Text":"What you see is a long chain,"},{"Start":"02:06.710 ","End":"02:11.675","Text":"then turned in based on the sequence into various proteins."},{"Start":"02:11.675 ","End":"02:14.735","Text":"This is how E. coli has this strand,"},{"Start":"02:14.735 ","End":"02:19.310","Text":"with a sequence that codes for multiple proteins,"},{"Start":"02:19.310 ","End":"02:21.920","Text":"in this case, more than 3,000 proteins."},{"Start":"02:21.920 ","End":"02:23.885","Text":"Now I\u0027m looking at"},{"Start":"02:23.885 ","End":"02:30.770","Text":"a more sophisticated or a more evolved or basically a eukaryotic organism."},{"Start":"02:30.770 ","End":"02:37.359","Text":"A human has about 20,000 genes encoding a much larger number of proteins."},{"Start":"02:37.359 ","End":"02:42.950","Text":"While here, you generally will have 3,000 genes coding for these proteins,"},{"Start":"02:42.950 ","End":"02:48.545","Text":"humans have 20,000 genes encoding a much larger number of protein."},{"Start":"02:48.545 ","End":"02:55.670","Text":"You\u0027d basically will see in humans that you have the DNA in"},{"Start":"02:55.670 ","End":"03:03.965","Text":"which this is the where the genes are coded that then can be transcribed into the RNA,"},{"Start":"03:03.965 ","End":"03:10.350","Text":"which from there is translated by ribosomes to proteins."},{"Start":"03:10.350 ","End":"03:15.920","Text":"You have these multiple genes that code for different proteins,"},{"Start":"03:15.920 ","End":"03:20.275","Text":"and you have a variety of proteins in a human."},{"Start":"03:20.275 ","End":"03:28.775","Text":"Somehow these sequences code for these different proteins that have different structures."},{"Start":"03:28.775 ","End":"03:33.220","Text":"The colors that you\u0027re seeing here is just to signify difference."},{"Start":"03:33.220 ","End":"03:36.380","Text":"The facts that demonstrate the link between amino acid sequence and"},{"Start":"03:36.380 ","End":"03:39.920","Text":"function are what we\u0027re going to talk about now."},{"Start":"03:39.920 ","End":"03:44.150","Text":"We\u0027re just going to talk about how this structure,"},{"Start":"03:44.150 ","End":"03:47.570","Text":"the primary structure, the amino acid sequence,"},{"Start":"03:47.570 ","End":"03:56.210","Text":"somehow goes over to affect the structure which in essence is associated to the function."},{"Start":"03:56.210 ","End":"04:00.710","Text":"Proteins with different functions always have different amino acid sequences."},{"Start":"04:00.710 ","End":"04:08.240","Text":"That gives us a hint to this association between function and sequence."},{"Start":"04:08.240 ","End":"04:11.300","Text":"Thousands of human genetic disorders have been"},{"Start":"04:11.300 ","End":"04:15.170","Text":"traced to the production of defective proteins."},{"Start":"04:15.170 ","End":"04:19.490","Text":"Genetic disorders, meaning something in the genes in"},{"Start":"04:19.490 ","End":"04:23.674","Text":"this sequences are associated with defective proteins."},{"Start":"04:23.674 ","End":"04:26.300","Text":"Again, relating genes,"},{"Start":"04:26.300 ","End":"04:31.940","Text":"and sequences to proteins plausibly structure and function,"},{"Start":"04:31.940 ","End":"04:39.605","Text":"eluding that there is this association or link between sequence and function."},{"Start":"04:39.605 ","End":"04:43.340","Text":"Now the defect can range from a single chain in the amino acid sequence"},{"Start":"04:43.340 ","End":"04:47.000","Text":"to deletion of a larger portion of the polypeptide chain,"},{"Start":"04:47.000 ","End":"04:49.280","Text":"meaning a whole sequence that\u0027s missing versus"},{"Start":"04:49.280 ","End":"04:53.960","Text":"just an amino acid that was changed even to something similar."},{"Start":"04:53.960 ","End":"04:59.720","Text":"Furthermore, upon comparison of functionally similar proteins from different species,"},{"Start":"04:59.720 ","End":"05:02.845","Text":"the proteins have similar amino acid sequences."},{"Start":"05:02.845 ","End":"05:07.865","Text":"Again, alluding to the fact that if there is a similar function,"},{"Start":"05:07.865 ","End":"05:10.085","Text":"there is a similar sequence."},{"Start":"05:10.085 ","End":"05:15.230","Text":"This strongly links the sequence of amino acids to the function,"},{"Start":"05:15.230 ","End":"05:18.520","Text":"and taking a step back, to genetic sequence."},{"Start":"05:18.520 ","End":"05:22.699","Text":"The amino acid sequence of a particular protein has some flexibility."},{"Start":"05:22.699 ","End":"05:27.620","Text":"An estimated 20, 30% of proteins in humans are polymorphic,"},{"Start":"05:27.620 ","End":"05:31.865","Text":"meaning having amino acid sequence of variance in the human population."},{"Start":"05:31.865 ","End":"05:33.920","Text":"What does variance actually mean?"},{"Start":"05:33.920 ","End":"05:35.180","Text":"Simplifying this further,"},{"Start":"05:35.180 ","End":"05:38.540","Text":"is that these proteins have a couple of"},{"Start":"05:38.540 ","End":"05:42.770","Text":"possible options of a sequence that code for the same proteins."},{"Start":"05:42.770 ","End":"05:47.330","Text":"If you look here, say humans that fall into mammals,"},{"Start":"05:47.330 ","End":"05:50.300","Text":"you can have 2 different codons,"},{"Start":"05:50.300 ","End":"05:56.285","Text":"2 different nucleic acid codons that code for the same amino acid."},{"Start":"05:56.285 ","End":"06:02.485","Text":"This is a variant of arginine and that is what polymorphic in essence means."},{"Start":"06:02.485 ","End":"06:06.765","Text":"You find this to be common, this protein flexibility."},{"Start":"06:06.765 ","End":"06:09.800","Text":"The amino acid sequence of a particular protein having"},{"Start":"06:09.800 ","End":"06:13.195","Text":"this flexibility due to these variations."},{"Start":"06:13.195 ","End":"06:16.370","Text":"Many of these variations in sequence have"},{"Start":"06:16.370 ","End":"06:19.820","Text":"little or no effect on the function of the protein."},{"Start":"06:19.820 ","End":"06:23.540","Text":"Furthermore, proteins that carry out similar function in"},{"Start":"06:23.540 ","End":"06:29.000","Text":"distantly related species can differ greatly in amino acid sequence and overall size."},{"Start":"06:29.000 ","End":"06:36.260","Text":"Meaning you can have similar function of proteins in different species that are distantly"},{"Start":"06:36.260 ","End":"06:40.040","Text":"related and the reason this information is mentioned is because it"},{"Start":"06:40.040 ","End":"06:44.605","Text":"means that they have evolved over time separately,"},{"Start":"06:44.605 ","End":"06:48.781","Text":"and their sequences and genetics have evolved to be different,"},{"Start":"06:48.781 ","End":"06:52.310","Text":"yet they still have these proteins that function similarly,"},{"Start":"06:52.310 ","End":"06:55.415","Text":"but the amino acid sequence and"},{"Start":"06:55.415 ","End":"07:01.260","Text":"overall size of the sequence are actually greatly different."},{"Start":"07:01.260 ","End":"07:05.360","Text":"The amino acid sequence in some regions of"},{"Start":"07:05.360 ","End":"07:11.615","Text":"the primary structure may vary considerably without affecting biological function."},{"Start":"07:11.615 ","End":"07:15.860","Text":"Most proteins contain crucial regions that are essential to their function,"},{"Start":"07:15.860 ","End":"07:19.115","Text":"and thus have sequences that are conserved."},{"Start":"07:19.115 ","End":"07:26.420","Text":"The fraction of the overall sequence that is critical varies from protein to protein."},{"Start":"07:26.420 ","End":"07:29.360","Text":"Complicating the task relating sequence to"},{"Start":"07:29.360 ","End":"07:32.150","Text":"3-dimensional structure and structure to function."},{"Start":"07:32.150 ","End":"07:35.150","Text":"Basically, this is saying that the portion of the genome that is crucial for"},{"Start":"07:35.150 ","End":"07:38.795","Text":"the protein\u0027s function can be 1% in 1 protein,"},{"Start":"07:38.795 ","End":"07:42.110","Text":"7% in another, or 20 in another,"},{"Start":"07:42.110 ","End":"07:45.500","Text":"so you\u0027d only look at the sequence and how much of it is conserved,"},{"Start":"07:45.500 ","End":"07:49.175","Text":"it may not reflect the same proportion,"},{"Start":"07:49.175 ","End":"07:52.400","Text":"magnitude, and significance in a protein."},{"Start":"07:52.400 ","End":"07:58.010","Text":"2 major discoveries in 1953 were of crucial importance in the history of biochemistry."},{"Start":"07:58.010 ","End":"08:01.685","Text":"In that year, James D. Watson and Francis Crick,"},{"Start":"08:01.685 ","End":"08:03.815","Text":"who we mentioned earlier on in the course,"},{"Start":"08:03.815 ","End":"08:05.930","Text":"deduced the structure of DNA,"},{"Start":"08:05.930 ","End":"08:10.010","Text":"and proposed a structural basis for its precise replication."},{"Start":"08:10.010 ","End":"08:16.504","Text":"We know Watson and Crick had suggested this helical shape of DNA."},{"Start":"08:16.504 ","End":"08:18.095","Text":"In that same year,"},{"Start":"08:18.095 ","End":"08:21.320","Text":"Frederick Sanger worked out the sequence of"},{"Start":"08:21.320 ","End":"08:25.625","Text":"amino acid residues in a polypeptide chains of the hormone insulin."},{"Start":"08:25.625 ","End":"08:27.950","Text":"Now today this may seem like an easy task,"},{"Start":"08:27.950 ","End":"08:30.710","Text":"but it was something that was very hard to do back then."},{"Start":"08:30.710 ","End":"08:33.920","Text":"The tools were not really exist in and actually"},{"Start":"08:33.920 ","End":"08:38.165","Text":"he is considered to be the father of sequencing."},{"Start":"08:38.165 ","End":"08:41.450","Text":"It quickly became evident that"},{"Start":"08:41.450 ","End":"08:44.270","Text":"the nucleotide sequence in DNA and"},{"Start":"08:44.270 ","End":"08:48.185","Text":"the amino acid sequence in proteins were somehow related."},{"Start":"08:48.185 ","End":"08:52.205","Text":"What you see here is actually Sanger sequencing or sequencing,"},{"Start":"08:52.205 ","End":"08:58.675","Text":"where you see the nucleic acids mentioned with this graph and in different colors,"},{"Start":"08:58.675 ","End":"09:01.370","Text":"and numbering system because that relates"},{"Start":"09:01.370 ","End":"09:05.830","Text":"the location of the nucleic acid to the location in the sequence."},{"Start":"09:05.830 ","End":"09:07.925","Text":"Barely a decade after these discoveries,"},{"Start":"09:07.925 ","End":"09:10.940","Text":"the role of a nucleotide sequence of DNA in determining"},{"Start":"09:10.940 ","End":"09:14.665","Text":"the amino acid sequence of protein molecules was revealed,"},{"Start":"09:14.665 ","End":"09:17.270","Text":"which enabled their elucidation,"},{"Start":"09:17.270 ","End":"09:22.520","Text":"so that today an enormous number of protein sequences can be"},{"Start":"09:22.520 ","End":"09:27.995","Text":"derived indirectly from the DNA sequences in the rapidly growing genome databases."},{"Start":"09:27.995 ","End":"09:31.400","Text":"Because once these are discovered and published,"},{"Start":"09:31.400 ","End":"09:32.840","Text":"they\u0027re added to database."},{"Start":"09:32.840 ","End":"09:38.375","Text":"Basically, we have this sequence relating the DNA template strand,"},{"Start":"09:38.375 ","End":"09:41.840","Text":"to the mRNA sequence to proteins and"},{"Start":"09:41.840 ","End":"09:46.070","Text":"their sequence with the primary sequence is actually the amino acid sequence."},{"Start":"09:46.070 ","End":"09:51.170","Text":"However, many are still deduced by traditional methods of polypeptide sequencing."},{"Start":"09:51.170 ","End":"09:55.880","Text":"The amino acid sequences have thousands of different proteins from many species have been"},{"Start":"09:55.880 ","End":"10:02.180","Text":"determined using principles first developed by Sanger, father of sequencing."},{"Start":"10:02.180 ","End":"10:04.400","Text":"These methods are still in use,"},{"Start":"10:04.400 ","End":"10:07.670","Text":"although with many variations and improvements in detail."},{"Start":"10:07.670 ","End":"10:11.750","Text":"I most definitely can say that as a molecular virologist and viral biochemists,"},{"Start":"10:11.750 ","End":"10:14.765","Text":"I use sequencing all the time and"},{"Start":"10:14.765 ","End":"10:18.890","Text":"not talking about deep sequencing, rather Sanger sequencing."},{"Start":"10:18.890 ","End":"10:23.345","Text":"This is a very current method that\u0027s still important."},{"Start":"10:23.345 ","End":"10:26.210","Text":"At this point, we\u0027ve completed this section on sequence and"},{"Start":"10:26.210 ","End":"10:29.285","Text":"protein function within amino acids, peptides and proteins."},{"Start":"10:29.285 ","End":"10:31.045","Text":"Characteristic of a protein sequence,"},{"Start":"10:31.045 ","End":"10:32.685","Text":"talking about the building blocks of it,"},{"Start":"10:32.685 ","End":"10:34.000","Text":"and amino acid sequence,"},{"Start":"10:34.000 ","End":"10:36.650","Text":"and the link between the genetic sequence and protein sequence,"},{"Start":"10:36.650 ","End":"10:43.140","Text":"and the link between the protein sequence and function has also been made."}],"ID":29401},{"Watched":false,"Name":"Exercise 1","Duration":"1m 56s","ChapterTopicVideoID":28169,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.890 ","End":"00:04.295","Text":"We are in Sequence and Protein Function,"},{"Start":"00:04.295 ","End":"00:06.955","Text":"an exercise testing our knowledge on this."},{"Start":"00:06.955 ","End":"00:10.180","Text":"We covered 3 specific facts that demonstrate the link"},{"Start":"00:10.180 ","End":"00:13.535","Text":"between amino acid sequence and function. List these."},{"Start":"00:13.535 ","End":"00:20.005","Text":"The facts that demonstrate the link between amino acid sequence and function are; 1,"},{"Start":"00:20.005 ","End":"00:24.955","Text":"proteins with different functions always have different amino acid sequences; 2,"},{"Start":"00:24.955 ","End":"00:28.030","Text":"thousands of human genetic disorders have been"},{"Start":"00:28.030 ","End":"00:31.540","Text":"traced to the production of defective proteins."},{"Start":"00:31.540 ","End":"00:34.150","Text":"The defect can range from a single change in"},{"Start":"00:34.150 ","End":"00:39.670","Text":"the amino acid sequence to deletion of a larger portion of the polypeptide chain."},{"Start":"00:39.670 ","End":"00:43.119","Text":"Hence, too, if a genetic disorder,"},{"Start":"00:43.119 ","End":"00:46.820","Text":"basically something wrong in the genes,"},{"Start":"00:46.820 ","End":"00:52.145","Text":"results in the fact that these individuals have defective proteins,"},{"Start":"00:52.145 ","End":"00:58.310","Text":"there is plausibly some link between the genes and the proteins."},{"Start":"00:58.310 ","End":"01:00.320","Text":"Now here, what is to say,"},{"Start":"01:00.320 ","End":"01:05.570","Text":"is it can be a single change in the amino acid sequence,"},{"Start":"01:05.570 ","End":"01:08.165","Text":"1 change in the sequence,"},{"Start":"01:08.165 ","End":"01:09.650","Text":"even a small 1,"},{"Start":"01:09.650 ","End":"01:11.480","Text":"can result in a disorder,"},{"Start":"01:11.480 ","End":"01:12.970","Text":"in a defective protein."},{"Start":"01:12.970 ","End":"01:17.015","Text":"Of course, you can have the case of a deletion of a large portion,"},{"Start":"01:17.015 ","End":"01:23.390","Text":"but this indicates that a small change can affect proteins,"},{"Start":"01:23.390 ","End":"01:25.490","Text":"a small change in the sequence, ever so minute,"},{"Start":"01:25.490 ","End":"01:33.535","Text":"can affect protein function and in essence cause a disorder."},{"Start":"01:33.535 ","End":"01:39.050","Text":"3, upon comparison of functionally similar proteins from different species,"},{"Start":"01:39.050 ","End":"01:42.080","Text":"the proteins have similar amino acid sequences."},{"Start":"01:42.080 ","End":"01:44.750","Text":"If you\u0027re going to see different species having"},{"Start":"01:44.750 ","End":"01:47.675","Text":"a protein that\u0027s similar in what it does,"},{"Start":"01:47.675 ","End":"01:49.669","Text":"if you go back and trace its sequence,"},{"Start":"01:49.669 ","End":"01:57.090","Text":"you will find similarity again indicating this link between sequence and function."}],"ID":29402},{"Watched":false,"Name":"Exercise 2","Duration":"3m 4s","ChapterTopicVideoID":28170,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.394","Text":"Hi there, we are within the topic of sequence and protein function."},{"Start":"00:04.394 ","End":"00:05.685","Text":"Let\u0027s test your knowledge."},{"Start":"00:05.685 ","End":"00:07.350","Text":"Which statement is true?"},{"Start":"00:07.350 ","End":"00:12.630","Text":"A. The amino acid sequence of a particular protein has some flexibility, b."},{"Start":"00:12.630 ","End":"00:15.855","Text":"20-30 percent of proteins in humans are polymorphic,"},{"Start":"00:15.855 ","End":"00:21.150","Text":"c. These variations in sequence have little or no effect on the function of a protein,"},{"Start":"00:21.150 ","End":"00:23.820","Text":"d. Proteins that carry out similar function in"},{"Start":"00:23.820 ","End":"00:28.350","Text":"distantly related species can differ greatly in amino acid sequence in overall size,"},{"Start":"00:28.350 ","End":"00:30.420","Text":"and e. All of the above."},{"Start":"00:30.420 ","End":"00:32.115","Text":"Let\u0027s practice 1 at a time."},{"Start":"00:32.115 ","End":"00:36.060","Text":"The amino acid sequence of a particular protein has some flexibility."},{"Start":"00:36.060 ","End":"00:41.015","Text":"We mentioned that there is some ability to have variants in variability,"},{"Start":"00:41.015 ","End":"00:45.800","Text":"and yet even with this variation in a sequence slight variation,"},{"Start":"00:45.800 ","End":"00:49.070","Text":"the protein can still be encoded."},{"Start":"00:49.070 ","End":"00:51.500","Text":"This statement is true."},{"Start":"00:51.500 ","End":"00:54.065","Text":"But let\u0027s move on and go check the rest."},{"Start":"00:54.065 ","End":"00:58.235","Text":"B. 20-30 percent of proteins in humans are polymorphic."},{"Start":"00:58.235 ","End":"01:02.450","Text":"If you remember, we mentioned the word polymorphic meaning having"},{"Start":"01:02.450 ","End":"01:07.160","Text":"amino acid sequence variants in the human population."},{"Start":"01:07.160 ","End":"01:09.845","Text":"These proteins in humans,"},{"Start":"01:09.845 ","End":"01:13.910","Text":"even though they can be the same protein, protein X,"},{"Start":"01:13.910 ","End":"01:20.110","Text":"it can have some variation in the amino acid sequence in individuals,"},{"Start":"01:20.110 ","End":"01:22.255","Text":"and about 20-30 percent,"},{"Start":"01:22.255 ","End":"01:27.305","Text":"yet it will still code for the same protein."},{"Start":"01:27.305 ","End":"01:29.555","Text":"This we know is true as well."},{"Start":"01:29.555 ","End":"01:34.355","Text":"Let\u0027s move on and see because we can jump and say all the above,"},{"Start":"01:34.355 ","End":"01:36.680","Text":"but maybe it\u0027s a matter of preciseness,"},{"Start":"01:36.680 ","End":"01:40.520","Text":"and we rather check the rest of our answers before we jump the gun."},{"Start":"01:40.520 ","End":"01:45.350","Text":"C. These variations in sequence have little or no effect on the function of the protein."},{"Start":"01:45.350 ","End":"01:50.420","Text":"We did say that many of these variations in actuality,"},{"Start":"01:50.420 ","End":"01:52.740","Text":"though there\u0027s variation in the sequence,"},{"Start":"01:52.740 ","End":"01:57.995","Text":"don\u0027t necessarily have an effect on the function of a protein."},{"Start":"01:57.995 ","End":"02:00.590","Text":"Again, this seems to be true."},{"Start":"02:00.590 ","End":"02:01.920","Text":"Let\u0027s just validate d,"},{"Start":"02:01.920 ","End":"02:05.310","Text":"before we jump over to e. Proteins that carry out similar function in"},{"Start":"02:05.310 ","End":"02:10.010","Text":"distantly related species can differ greatly in amino acid sequence in overall size."},{"Start":"02:10.010 ","End":"02:11.600","Text":"On the 1 hand,"},{"Start":"02:11.600 ","End":"02:16.940","Text":"we said that if you find similar protein function in different organisms,"},{"Start":"02:16.940 ","End":"02:22.460","Text":"they tend to have similar amino acid sequence or similar genetic sequence,"},{"Start":"02:22.460 ","End":"02:25.880","Text":"yet we also said that proteins that carry"},{"Start":"02:25.880 ","End":"02:29.480","Text":"out similar function in distantly related species,"},{"Start":"02:29.480 ","End":"02:35.095","Text":"meaning they\u0027ve evolved to become quite different over time,"},{"Start":"02:35.095 ","End":"02:37.160","Text":"this means their sequences,"},{"Start":"02:37.160 ","End":"02:38.975","Text":"even for the same things,"},{"Start":"02:38.975 ","End":"02:42.605","Text":"have changed, so they can result in a similar function,"},{"Start":"02:42.605 ","End":"02:49.295","Text":"but the sequence can actually be different and even differ greatly and in size."},{"Start":"02:49.295 ","End":"02:51.680","Text":"This is true as well."},{"Start":"02:51.680 ","End":"02:54.080","Text":"If we answer any 1 of these,"},{"Start":"02:54.080 ","End":"02:56.480","Text":"it would be incorrect because they\u0027re all true,"},{"Start":"02:56.480 ","End":"03:00.455","Text":"so we don\u0027t want to take any of these on account,"},{"Start":"03:00.455 ","End":"03:04.440","Text":"and rather, the answer is all of the above."}],"ID":29403},{"Watched":false,"Name":"Exercise 3","Duration":"3m 33s","ChapterTopicVideoID":28171,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.020 ","End":"00:05.265","Text":"Welcome back to another exercise on sequence and protein function."},{"Start":"00:05.265 ","End":"00:08.534","Text":"What can be said about the flexibility of a protein sequence?"},{"Start":"00:08.534 ","End":"00:11.070","Text":"We said a number of things in the lesson,"},{"Start":"00:11.070 ","End":"00:16.245","Text":"so let\u0027s remind ourselves of this and whatever of this you remembered, kudos to you."},{"Start":"00:16.245 ","End":"00:17.715","Text":"Hopefully you remembered it all."},{"Start":"00:17.715 ","End":"00:20.250","Text":"Let\u0027s start with the fact that the amino acid sequence of"},{"Start":"00:20.250 ","End":"00:22.965","Text":"a particular protein has some flexibility."},{"Start":"00:22.965 ","End":"00:28.020","Text":"What this means is that the same protein can have some variation in"},{"Start":"00:28.020 ","End":"00:33.023","Text":"the amino acid sequence and still have the same intended function,"},{"Start":"00:33.023 ","End":"00:34.635","Text":"and in connection with this,"},{"Start":"00:34.635 ","End":"00:40.005","Text":"we mentioned that an estimated 20-30 percent of proteins in humans are polymorphic,"},{"Start":"00:40.005 ","End":"00:43.549","Text":"meaning have an amino acid sequence variants in the human population,"},{"Start":"00:43.549 ","End":"00:48.485","Text":"and we give an example here in humans that the codon AGA and AGG."},{"Start":"00:48.485 ","End":"00:57.170","Text":"These are 3 different sequences of nucleic acids that code for an amino acid, arginine."},{"Start":"00:57.170 ","End":"01:04.820","Text":"These 2 different ones code for the same amino acid and you see the same redundancy,"},{"Start":"01:04.820 ","End":"01:11.030","Text":"the same similarity of having some variants coding for the same amino acid."},{"Start":"01:11.030 ","End":"01:17.285","Text":"We see this as well in sequences of amino acids that have some redundancy"},{"Start":"01:17.285 ","End":"01:24.275","Text":"or ability to be varied or change and code for the same protein."},{"Start":"01:24.275 ","End":"01:27.290","Text":"We also mentioned that many of these variations in sequence have"},{"Start":"01:27.290 ","End":"01:30.185","Text":"little or no effect on the function of the protein."},{"Start":"01:30.185 ","End":"01:35.575","Text":"This accounting again for flexibility of a protein sequence."},{"Start":"01:35.575 ","End":"01:38.570","Text":"Furthermore, proteins that carry out similar function in"},{"Start":"01:38.570 ","End":"01:43.415","Text":"distantly related species can differ greatly in amino acid sequence and overall size."},{"Start":"01:43.415 ","End":"01:46.265","Text":"Again, you\u0027re seeing a case that there\u0027s a similar function."},{"Start":"01:46.265 ","End":"01:48.470","Text":"But these species that are distantly related,"},{"Start":"01:48.470 ","End":"01:50.390","Text":"meaning they\u0027ve evolved from"},{"Start":"01:50.390 ","End":"01:52.980","Text":"a common ancestor and"},{"Start":"01:52.980 ","End":"01:57.020","Text":"a long time has passed and they\u0027ve evolved to be different from each other,"},{"Start":"01:57.020 ","End":"02:01.310","Text":"they also differ greatly in amino acid sequence and overall size."},{"Start":"02:01.310 ","End":"02:03.650","Text":"Though the function of the protein is similar,"},{"Start":"02:03.650 ","End":"02:06.065","Text":"probably because it\u0027s necessary for function."},{"Start":"02:06.065 ","End":"02:08.420","Text":"In addition, while the amino acid sequence in"},{"Start":"02:08.420 ","End":"02:11.930","Text":"some regions vary considerably without affecting biological function,"},{"Start":"02:11.930 ","End":"02:14.240","Text":"we see that proteins contain crucial regions that are"},{"Start":"02:14.240 ","End":"02:17.405","Text":"essential to their function and thus are conserved."},{"Start":"02:17.405 ","End":"02:20.810","Text":"Even though there is flexibility,"},{"Start":"02:20.810 ","End":"02:22.850","Text":"that you\u0027re seeing some regions are different or whatever,"},{"Start":"02:22.850 ","End":"02:25.940","Text":"there are certain regions that stay conserved,"},{"Start":"02:25.940 ","End":"02:27.920","Text":"they stay the same or similar,"},{"Start":"02:27.920 ","End":"02:33.605","Text":"and these are generally crucial for biological function,"},{"Start":"02:33.605 ","End":"02:37.160","Text":"and therefore that part is important for conservation,"},{"Start":"02:37.160 ","End":"02:40.790","Text":"for staying similar and not having varying effect."},{"Start":"02:40.790 ","End":"02:44.960","Text":"While we\u0027re seeing variation of flexibility,"},{"Start":"02:44.960 ","End":"02:49.490","Text":"some important regions are staying similar or the same, yet, in total,"},{"Start":"02:49.490 ","End":"02:51.350","Text":"when we grasp the protein sequence,"},{"Start":"02:51.350 ","End":"02:54.350","Text":"we\u0027re seeing variability flexibility."},{"Start":"02:54.350 ","End":"02:56.690","Text":"Now, the fraction of the overall sequence that is"},{"Start":"02:56.690 ","End":"02:59.150","Text":"critical varies from protein to protein."},{"Start":"02:59.150 ","End":"03:02.630","Text":"This complicating the task of relating sequence to 3-dimensional structure,"},{"Start":"03:02.630 ","End":"03:03.905","Text":"and structure to function."},{"Start":"03:03.905 ","End":"03:06.485","Text":"But this also means that when looking at it,"},{"Start":"03:06.485 ","End":"03:08.825","Text":"we\u0027re seeing variability and flexibility."},{"Start":"03:08.825 ","End":"03:11.870","Text":"Basically, this is saying that the portion of the genome that"},{"Start":"03:11.870 ","End":"03:14.750","Text":"is crucial for the protein\u0027s function can be 1 percent in 1 protein,"},{"Start":"03:14.750 ","End":"03:16.265","Text":"7 percent in another,"},{"Start":"03:16.265 ","End":"03:18.020","Text":"or 20 percent in another,"},{"Start":"03:18.020 ","End":"03:21.260","Text":"thus allowing for even more flexibility when looking at"},{"Start":"03:21.260 ","End":"03:24.860","Text":"the sequence and the protein it codes for."},{"Start":"03:24.860 ","End":"03:28.130","Text":"Now all of these points come together to tell us"},{"Start":"03:28.130 ","End":"03:33.269","Text":"that there is flexibility in a protein sequence."}],"ID":29404},{"Watched":false,"Name":"Exercise 4","Duration":"1m 51s","ChapterTopicVideoID":28172,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.260","Text":"Let\u0027s dive into another exercise within sequence and protein function."},{"Start":"00:04.260 ","End":"00:06.630","Text":"2 major discoveries were mentioned in relevance to"},{"Start":"00:06.630 ","End":"00:09.585","Text":"the understanding of the link between genetics and proteins."},{"Start":"00:09.585 ","End":"00:10.920","Text":"But were these, and what was"},{"Start":"00:10.920 ","End":"00:13.725","Text":"their important contribution in the history of both constraints."},{"Start":"00:13.725 ","End":"00:16.620","Text":"The 2 major discoveries in 1953 that were of"},{"Start":"00:16.620 ","End":"00:20.055","Text":"crucial importance in the history of biochemistry are;"},{"Start":"00:20.055 ","End":"00:24.690","Text":"1 was by James D. Watson and Francis Crick who deduced the structure of DNA."},{"Start":"00:24.690 ","End":"00:28.200","Text":"Just to remind you if there is a third counterpart to this,"},{"Start":"00:28.200 ","End":"00:30.845","Text":"if you don\u0027t remember her name, please go back."},{"Start":"00:30.845 ","End":"00:33.470","Text":"She did not get credit with a Nobel Prize for her work,"},{"Start":"00:33.470 ","End":"00:37.627","Text":"but she contributed greatly to this, just an FYI."},{"Start":"00:37.627 ","End":"00:41.600","Text":"The second major discovery was of Frederick Sanger who worked out"},{"Start":"00:41.600 ","End":"00:46.579","Text":"the sequence of amino acid residues in a polypeptide chains of the hormone insulin."},{"Start":"00:46.579 ","End":"00:52.190","Text":"What you see here is the alluded structure of DNA that came from Crick, Watson,"},{"Start":"00:52.190 ","End":"00:53.870","Text":"and Wilkins work that they\u0027ve gotten"},{"Start":"00:53.870 ","End":"00:56.930","Text":"Nobel Prize for and you have this helical structure,"},{"Start":"00:56.930 ","End":"01:00.195","Text":"and you have a sequence here,"},{"Start":"01:00.195 ","End":"01:02.930","Text":"this is the idea of Sanger sequencing where you see"},{"Start":"01:02.930 ","End":"01:07.720","Text":"each nucleotide with a specific position and a continuous sequence."},{"Start":"01:07.720 ","End":"01:13.100","Text":"This actually, you see numbers here and these indicate the position in the sequence."},{"Start":"01:13.100 ","End":"01:16.940","Text":"This led to the understanding that the nucleotide sequence in DNA"},{"Start":"01:16.940 ","End":"01:20.840","Text":"and the amino acid sequence in proteins were somehow related."},{"Start":"01:20.840 ","End":"01:24.230","Text":"Less than a decade later, the role of the nucleotide sequence of a DNA in"},{"Start":"01:24.230 ","End":"01:27.800","Text":"determining the amino acid sequence of protein molecules was revealed,"},{"Start":"01:27.800 ","End":"01:33.035","Text":"resulting in the ability to derive protein sequences indirectly from the DNA sequences."},{"Start":"01:33.035 ","End":"01:36.395","Text":"When sequencing DNA, basically taking a gene and sequencing it,"},{"Start":"01:36.395 ","End":"01:40.340","Text":"you can derive a protein sequence from it."},{"Start":"01:40.340 ","End":"01:41.630","Text":"There\u0027s a relationship."},{"Start":"01:41.630 ","End":"01:44.255","Text":"It\u0027s basically a codebook for proteins."},{"Start":"01:44.255 ","End":"01:46.040","Text":"You have the DNA sequence that codes for,"},{"Start":"01:46.040 ","End":"01:50.790","Text":"meaning in amino acid sequence and this codes for the protein."}],"ID":29405},{"Watched":false,"Name":"Sequence and Biochemical Information Part 1","Duration":"8m 43s","ChapterTopicVideoID":28173,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.868","Text":"Hi there. Welcome back to Sequence and Proteins."},{"Start":"00:04.868 ","End":"00:08.835","Text":"Now we\u0027re going to talk about sequence and biochemical information."},{"Start":"00:08.835 ","End":"00:10.110","Text":"By the end of this section,"},{"Start":"00:10.110 ","End":"00:14.040","Text":"you\u0027ll describe the link between protein sequence and biochemical information,"},{"Start":"00:14.040 ","End":"00:18.548","Text":"understand the link between amino acid sequence and evolutionary relationships,"},{"Start":"00:18.548 ","End":"00:20.860","Text":"and comprehend protein family assignment."},{"Start":"00:20.860 ","End":"00:24.410","Text":"Amino acid sequence provides biochemical information,"},{"Start":"00:24.410 ","End":"00:26.765","Text":"and in essence, structural information."},{"Start":"00:26.765 ","End":"00:29.810","Text":"Knowledge of the sequence of amino acids in a protein can offer"},{"Start":"00:29.810 ","End":"00:33.500","Text":"insights into the 3-dimensional structure and its function,"},{"Start":"00:33.500 ","End":"00:35.810","Text":"cellular location, and evolution."},{"Start":"00:35.810 ","End":"00:41.525","Text":"Most of these insights are derived by comparing similarities with other known sequences."},{"Start":"00:41.525 ","End":"00:47.930","Text":"We\u0027re connecting this to the previous lesson and diving deeper into it."},{"Start":"00:47.930 ","End":"00:50.150","Text":"Thousands of sequences are known and available"},{"Start":"00:50.150 ","End":"00:52.715","Text":"in databases accessible through the Internet."},{"Start":"00:52.715 ","End":"00:57.305","Text":"You can basically look at a sequence that you\u0027re interested in and"},{"Start":"00:57.305 ","End":"01:03.090","Text":"compare to the databases and then infer relationships."},{"Start":"01:03.090 ","End":"01:06.770","Text":"A comparison of newly obtained sequence"},{"Start":"01:06.770 ","End":"01:11.000","Text":"with this large bank of storage sequences reveals relationships."},{"Start":"01:11.000 ","End":"01:14.390","Text":"We\u0027re looking at this protein sequence,"},{"Start":"01:14.390 ","End":"01:15.620","Text":"the amino acid sequence."},{"Start":"01:15.620 ","End":"01:18.950","Text":"We take it and we then compare to"},{"Start":"01:18.950 ","End":"01:23.345","Text":"known sequences that are stored and have been discovered previously,"},{"Start":"01:23.345 ","End":"01:27.440","Text":"and then you can see it was similar to a known protein."},{"Start":"01:27.440 ","End":"01:30.664","Text":"Now this comparison often reveals"},{"Start":"01:30.664 ","End":"01:35.180","Text":"surprising and informative relationships between proteins."},{"Start":"01:35.180 ","End":"01:37.700","Text":"Exactly how the amino acid sequence determines"},{"Start":"01:37.700 ","End":"01:40.505","Text":"3-dimensional structure is not understood in detail."},{"Start":"01:40.505 ","End":"01:42.650","Text":"We know there\u0027s the structure primary,"},{"Start":"01:42.650 ","End":"01:44.395","Text":"the amino acid sequence."},{"Start":"01:44.395 ","End":"01:47.919","Text":"Then it organizes into the Alpha or Beta helices,"},{"Start":"01:47.919 ","End":"01:50.795","Text":"this arrangement of the amino acid chain,"},{"Start":"01:50.795 ","End":"01:52.460","Text":"and then it folds."},{"Start":"01:52.460 ","End":"01:54.755","Text":"This is the polypeptide chain, it folds,"},{"Start":"01:54.755 ","End":"01:57.965","Text":"and this is the tertiary structure versus here secondary structure."},{"Start":"01:57.965 ","End":"02:01.888","Text":"Now, how this really creates the folding can be predicted,"},{"Start":"02:01.888 ","End":"02:06.335","Text":"and there\u0027s a lot of biochemical and chemists that study this,"},{"Start":"02:06.335 ","End":"02:10.220","Text":"yet predictions aren\u0027t necessarily the reality."},{"Start":"02:10.220 ","End":"02:12.545","Text":"While there is a prediction,"},{"Start":"02:12.545 ","End":"02:17.295","Text":"the details of the 3-dimensional structure as hinted,"},{"Start":"02:17.295 ","End":"02:22.070","Text":"alluded predicted, from the amino acid sequence is not necessarily a direct science."},{"Start":"02:22.070 ","End":"02:26.000","Text":"Protein families that have some shared structural or functional features can be"},{"Start":"02:26.000 ","End":"02:30.500","Text":"readily identified on the basis of amino acid sequence similarities,"},{"Start":"02:30.500 ","End":"02:34.460","Text":"yet the structure is still something that is being studied ongoing"},{"Start":"02:34.460 ","End":"02:38.450","Text":"with crystallography, electron microscopy, etc."},{"Start":"02:38.450 ","End":"02:41.090","Text":"Individual proteins are assigned to families based on"},{"Start":"02:41.090 ","End":"02:44.330","Text":"the degree of similarity in amino acid sequence."},{"Start":"02:44.330 ","End":"02:50.810","Text":"Members of a family are typically identical across 25 percent or more of their sequences"},{"Start":"02:50.810 ","End":"02:54.530","Text":"and proteins in these families usually share"},{"Start":"02:54.530 ","End":"02:58.145","Text":"at least some structural and functional characteristics."},{"Start":"02:58.145 ","End":"03:00.410","Text":"Some families are, however,"},{"Start":"03:00.410 ","End":"03:03.590","Text":"defined by identities involving"},{"Start":"03:03.590 ","End":"03:08.769","Text":"only a few amino acid residues that are critical to a certain function."},{"Start":"03:08.769 ","End":"03:13.145","Text":"These amino acid residues are similar between"},{"Start":"03:13.145 ","End":"03:15.860","Text":"the different members of the families because these are the ones"},{"Start":"03:15.860 ","End":"03:19.169","Text":"that are more linked to the function,"},{"Start":"03:19.169 ","End":"03:22.880","Text":"while the other amino acids in that protein,"},{"Start":"03:22.880 ","End":"03:24.365","Text":"in the sequence,"},{"Start":"03:24.365 ","End":"03:26.960","Text":"that are not significant for the function over time and"},{"Start":"03:26.960 ","End":"03:31.370","Text":"evolution have more flexibility and ability to change."},{"Start":"03:31.370 ","End":"03:36.570","Text":"A number of similar substructures to be defined in another chapters,"},{"Start":"03:36.570 ","End":"03:40.545","Text":"domains, occur in many functionally unrelated proteins."},{"Start":"03:40.545 ","End":"03:43.640","Text":"These domains often fold into structural configurations that have"},{"Start":"03:43.640 ","End":"03:47.660","Text":"an unusual degree of stability or they\u0027re specialized for a certain environment."},{"Start":"03:47.660 ","End":"03:49.190","Text":"Looking at the gene sequence."},{"Start":"03:49.190 ","End":"03:52.360","Text":"But the gene sequence also codes for the amino acid sequence."},{"Start":"03:52.360 ","End":"03:56.260","Text":"In essence, this represents the amino acid sequence as well."},{"Start":"03:56.260 ","End":"03:58.339","Text":"When we\u0027re looking at the relationships,"},{"Start":"03:58.339 ","End":"04:01.025","Text":"we know there\u0027s the common relationship here."},{"Start":"04:01.025 ","End":"04:02.675","Text":"This is where they\u0027ve evolved from."},{"Start":"04:02.675 ","End":"04:04.875","Text":"Now you have the Alpha chain and Beta chain."},{"Start":"04:04.875 ","End":"04:06.200","Text":"Bottom line is to say,"},{"Start":"04:06.200 ","End":"04:07.280","Text":"when you\u0027re looking here,"},{"Start":"04:07.280 ","End":"04:13.050","Text":"these 2 are more similar in the sequence than these ones."},{"Start":"04:13.050 ","End":"04:15.440","Text":"Again, looking at amino acid sequence,"},{"Start":"04:15.440 ","End":"04:20.775","Text":"when you find these to be more similar than these in comparison to this one,"},{"Start":"04:20.775 ","End":"04:25.715","Text":"then you know that these are in a closer evolutionary relationship."},{"Start":"04:25.715 ","End":"04:27.962","Text":"The primary structure of a given protein from"},{"Start":"04:27.962 ","End":"04:31.535","Text":"related species closely resemble one another."},{"Start":"04:31.535 ","End":"04:33.830","Text":"If you see related species,"},{"Start":"04:33.830 ","End":"04:37.295","Text":"their sequence of amino acid, the amino acid residues,"},{"Start":"04:37.295 ","End":"04:43.895","Text":"will be more similar than species that are farther apart in the course of evolution."},{"Start":"04:43.895 ","End":"04:47.820","Text":"If you look at this versus this,"},{"Start":"04:47.820 ","End":"04:51.200","Text":"these are farther apart than this versus this."},{"Start":"04:51.200 ","End":"04:53.435","Text":"Consider the example of cytochrome c,"},{"Start":"04:53.435 ","End":"04:56.570","Text":"a protein found in nearly all eukaryotes."},{"Start":"04:56.570 ","End":"05:00.170","Text":"It is a component of the mitochondrial electron transport system,"},{"Start":"05:00.170 ","End":"05:03.230","Text":"which is believed to have taken its present form between"},{"Start":"05:03.230 ","End":"05:07.250","Text":"1.5-2 billion years ago when organisms developed aerobic respiration."},{"Start":"05:07.250 ","End":"05:08.930","Text":"It is similar in sequence as seen in"},{"Start":"05:08.930 ","End":"05:12.830","Text":"more than 100 eukaryotic species ranging in complexity from yeast to humans,"},{"Start":"05:12.830 ","End":"05:18.047","Text":"and they are single polypeptides of 104-112 residues."},{"Start":"05:18.047 ","End":"05:20.690","Text":"In accordance with evolutionary theory which indicates"},{"Start":"05:20.690 ","End":"05:24.838","Text":"related species have evolved from a common ancestor,"},{"Start":"05:24.838 ","End":"05:28.100","Text":"the genes with similar structures specifying each of their proteins must"},{"Start":"05:28.100 ","End":"05:32.550","Text":"likewise have evolved from the corresponding gene in that ancestor."},{"Start":"05:32.550 ","End":"05:37.670","Text":"Just as we looked at this tree which we introduced in the first chapter,"},{"Start":"05:37.670 ","End":"05:40.220","Text":"the idea of evolutionary relationships,"},{"Start":"05:40.220 ","End":"05:46.870","Text":"that you can actually see from these lines the similarity and the connection."},{"Start":"05:46.870 ","End":"05:51.710","Text":"These two came from a common ancestor about here in evolution."},{"Start":"05:51.710 ","End":"05:56.550","Text":"These two, they had a common ancestor here, etc."},{"Start":"05:56.550 ","End":"05:59.200","Text":"This infers relationship,"},{"Start":"05:59.200 ","End":"06:03.230","Text":"whereas if you\u0027re looking at this and this,"},{"Start":"06:03.230 ","End":"06:07.807","Text":"they have evolved over time and are much more different."},{"Start":"06:07.807 ","End":"06:11.975","Text":"This will not only be in the genetic sequence,"},{"Start":"06:11.975 ","End":"06:16.730","Text":"it will also be represented in the protein sequence."},{"Start":"06:16.730 ","End":"06:22.490","Text":"Certain amino acid sequences serve as signals that determine the cellular location,"},{"Start":"06:22.490 ","End":"06:25.775","Text":"chemical modification, and half-life of a protein."},{"Start":"06:25.775 ","End":"06:30.350","Text":"Special signal sequences usually at the amino terminus are used to target"},{"Start":"06:30.350 ","End":"06:31.970","Text":"certain proteins for export from"},{"Start":"06:31.970 ","End":"06:35.315","Text":"a cell or other proteins are targeted for distribution to the nucleus,"},{"Start":"06:35.315 ","End":"06:36.920","Text":"the cell surface, the cytosol,"},{"Start":"06:36.920 ","End":"06:38.435","Text":"and other cellular locations."},{"Start":"06:38.435 ","End":"06:42.080","Text":"Other sequences act as attachment sites for prosthetic groups."},{"Start":"06:42.080 ","End":"06:43.310","Text":"Just to remind you that this is"},{"Start":"06:43.310 ","End":"06:47.120","Text":"a non-protein group that is part or combined with a protein,"},{"Start":"06:47.120 ","End":"06:51.440","Text":"or another way to maybe explain it is by saying it\u0027s the non amino acid component"},{"Start":"06:51.440 ","End":"06:55.910","Text":"that is part of the structure of the hetero protein or conjugated protein."},{"Start":"06:55.910 ","End":"07:00.050","Text":"This is touching up on the terms that we mentioned before."},{"Start":"07:00.050 ","End":"07:03.500","Text":"The conjugated protein, which is a protein that has"},{"Start":"07:03.500 ","End":"07:11.870","Text":"both an amino acid portion and a non amino acid portion prosthetic group,"},{"Start":"07:11.870 ","End":"07:13.950","Text":"which we hadn\u0027t mentioned,"},{"Start":"07:13.950 ","End":"07:21.785","Text":"but this conjugated protein can also be referred to as a hetero protein."},{"Start":"07:21.785 ","End":"07:24.435","Text":"Remember, hetero, different."},{"Start":"07:24.435 ","End":"07:26.120","Text":"It\u0027s not just amino acids."},{"Start":"07:26.120 ","End":"07:30.950","Text":"Going back, some sequences has the attachment site for these prosthetic groups."},{"Start":"07:30.950 ","End":"07:34.595","Text":"They basically allow for the attachment"},{"Start":"07:34.595 ","End":"07:38.340","Text":"and the flag for a sugar group and a glycoprotein,"},{"Start":"07:38.340 ","End":"07:40.780","Text":"or a lipid and lipoprotein to attach there."},{"Start":"07:40.780 ","End":"07:43.430","Text":"Some of these signals are well-characterized and are"},{"Start":"07:43.430 ","End":"07:46.580","Text":"easily recognized in a sequence of a newly characterized protein."},{"Start":"07:46.580 ","End":"07:47.915","Text":"You get a new protein,"},{"Start":"07:47.915 ","End":"07:49.610","Text":"you find out its sequence,"},{"Start":"07:49.610 ","End":"07:53.065","Text":"and then you see, this sequence is familiar."},{"Start":"07:53.065 ","End":"07:57.510","Text":"This says, let\u0027s attach a sugar right here."},{"Start":"07:57.510 ","End":"08:03.230","Text":"Then it can be assumed that this sequence will result in a glycoprotein,"},{"Start":"08:03.230 ","End":"08:06.320","Text":"a protein that has a sugar prosthetic group attached to it."},{"Start":"08:06.320 ","End":"08:09.860","Text":"Tying this into things we had mentioned in previous lessons,"},{"Start":"08:09.860 ","End":"08:14.780","Text":"the simple string of letters denoting the amino acid sequence of a given protein,"},{"Start":"08:14.780 ","End":"08:18.005","Text":"elucidates its 3-dimensional structure,"},{"Start":"08:18.005 ","End":"08:21.500","Text":"which is determined largely by its primary structure,"},{"Start":"08:21.500 ","End":"08:26.330","Text":"as well as ultimately how life evolved on this planet."},{"Start":"08:26.330 ","End":"08:28.970","Text":"With this, we\u0027ve completed this portion,"},{"Start":"08:28.970 ","End":"08:33.140","Text":"sequence and biochemical information within sequence and proteins,"},{"Start":"08:33.140 ","End":"08:37.463","Text":"and we described the link between protein sequences and biochemical information,"},{"Start":"08:37.463 ","End":"08:38.810","Text":"we should understand the link between"},{"Start":"08:38.810 ","End":"08:40.925","Text":"amino acid sequence and evolutionary relationships,"},{"Start":"08:40.925 ","End":"08:44.190","Text":"and comprehend protein family assignment."}],"ID":29406},{"Watched":false,"Name":"Sequence and Biochemical Information Part 2","Duration":"3m 59s","ChapterTopicVideoID":28165,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.190","Text":"Consider the example of cytochrome c,"},{"Start":"00:02.190 ","End":"00:05.475","Text":"a protein found in nearly all eukaryotes."},{"Start":"00:05.475 ","End":"00:09.180","Text":"It is a component of the mitochondrial electron transport system"},{"Start":"00:09.180 ","End":"00:10.560","Text":"which is believed to have taken"},{"Start":"00:10.560 ","End":"00:13.020","Text":"its present form between 1 and 1.2-2 billion"},{"Start":"00:13.020 ","End":"00:16.140","Text":"years ago when organisms developed aerobic respiration."},{"Start":"00:16.140 ","End":"00:17.820","Text":"It is similar in sequence as seen in"},{"Start":"00:17.820 ","End":"00:21.753","Text":"more than 100 eukaryotic species raging in complexity from yeast to humans,"},{"Start":"00:21.753 ","End":"00:27.105","Text":"and there are single poly peptides of 104-112 residues."},{"Start":"00:27.105 ","End":"00:29.580","Text":"In accordance with evolutionary theory which indicates"},{"Start":"00:29.580 ","End":"00:33.569","Text":"related species have evolved from a common ancestor,"},{"Start":"00:33.569 ","End":"00:36.990","Text":"the genes with similar structure specifying each of their proteins must"},{"Start":"00:36.990 ","End":"00:40.470","Text":"likewise have evolved from the corresponding gene in that ancestor."},{"Start":"00:40.470 ","End":"00:48.358","Text":"Just as we look at this tree which we introduced in the 1st chapter;"},{"Start":"00:48.358 ","End":"00:54.640","Text":"the idea of evolutionary relationships that you can actually see from these lines,"},{"Start":"00:54.640 ","End":"00:57.843","Text":"the similarity and the connection,"},{"Start":"00:57.843 ","End":"01:02.800","Text":"these 2 came from a common ancestor about here in evolution."},{"Start":"01:02.800 ","End":"01:07.315","Text":"These 2 they had a common ancestor here, et cetera."},{"Start":"01:07.315 ","End":"01:14.425","Text":"This infers relationship whereas if you\u0027re looking at this and this,"},{"Start":"01:14.425 ","End":"01:19.490","Text":"they have evolved over time and are much more different."},{"Start":"01:19.490 ","End":"01:23.865","Text":"This will not only be in the genetic sequence,"},{"Start":"01:23.865 ","End":"01:29.780","Text":"it will also be represented in the protein sequence."},{"Start":"01:29.780 ","End":"01:36.110","Text":"Certain amino acid sequences serve as signals that determine the cellular location,"},{"Start":"01:36.110 ","End":"01:39.395","Text":"chemical modification, and half-life of a protein."},{"Start":"01:39.395 ","End":"01:43.970","Text":"Special signal sequences usually at the amino terminus are used to target"},{"Start":"01:43.970 ","End":"01:46.340","Text":"certain proteins for expert from a cell or"},{"Start":"01:46.340 ","End":"01:48.935","Text":"other proteins are targeted for distribution to the nucleus,"},{"Start":"01:48.935 ","End":"01:52.070","Text":"the cell surface, the cytosol on other cellular locations."},{"Start":"01:52.070 ","End":"01:55.705","Text":"Other sequences act as attachment sites for prosthetic groups."},{"Start":"01:55.705 ","End":"01:59.289","Text":"Just to remind you that this is a non-protein group that is part,"},{"Start":"01:59.289 ","End":"02:03.340","Text":"or combined with a protein or another way to maybe explain it is by saying it\u0027s"},{"Start":"02:03.340 ","End":"02:05.650","Text":"the non-amino acid component that is part of"},{"Start":"02:05.650 ","End":"02:09.520","Text":"the structure of the heteroprotein or conjugated protein."},{"Start":"02:09.520 ","End":"02:13.960","Text":"This is touching up on the terms that we mentioned before,"},{"Start":"02:13.960 ","End":"02:20.500","Text":"the conjugated protein which is a protein that has both an amino acid portion"},{"Start":"02:20.500 ","End":"02:27.748","Text":"and a non-amino acid portion; a prosthetic group."},{"Start":"02:27.748 ","End":"02:35.700","Text":"This conjugated protein can also be referred to as a heteroprotein."},{"Start":"02:35.700 ","End":"02:38.240","Text":"Remember hetero, different."},{"Start":"02:38.240 ","End":"02:41.070","Text":"It\u0027s not just amino acids going back,"},{"Start":"02:41.070 ","End":"02:45.305","Text":"some sequences has the attachment site for these prosthetic groups."},{"Start":"02:45.305 ","End":"02:49.865","Text":"They basically allow for the attachment and"},{"Start":"02:49.865 ","End":"02:55.730","Text":"the flag for a sugar group and a glycoprotein or lipid and lipoprotein to attach there."},{"Start":"02:55.730 ","End":"02:58.400","Text":"Some of these signals are well-characterized and are"},{"Start":"02:58.400 ","End":"03:01.400","Text":"easily recognized in a sequence of a newly characterized protein."},{"Start":"03:01.400 ","End":"03:02.885","Text":"You get a new protein,"},{"Start":"03:02.885 ","End":"03:08.275","Text":"you find out its sequence and then you see this sequence is familiar."},{"Start":"03:08.275 ","End":"03:10.225","Text":"This says, \"Okay,"},{"Start":"03:10.225 ","End":"03:12.662","Text":"let\u0027s attach a sugar right here.\""},{"Start":"03:12.662 ","End":"03:18.440","Text":"Then it could be assumed that this sequence will result in a glycoprotein,"},{"Start":"03:18.440 ","End":"03:21.200","Text":"a protein that has a sugar prosthetic group attached to it."},{"Start":"03:21.200 ","End":"03:25.389","Text":"Tying this into things we had mentioned in previous lessons,"},{"Start":"03:25.389 ","End":"03:27.920","Text":"the simple string of letters denoting"},{"Start":"03:27.920 ","End":"03:31.760","Text":"the amino acid sequence of a given protein elucidates it\u0027s"},{"Start":"03:31.760 ","End":"03:35.660","Text":"3-dimensional structure which is determined largely by"},{"Start":"03:35.660 ","End":"03:41.945","Text":"its primary structure as well as ultimately how life evolved on this planet."},{"Start":"03:41.945 ","End":"03:44.449","Text":"With this we\u0027ve completed this portion;"},{"Start":"03:44.449 ","End":"03:49.010","Text":"sequence and biochemical information within sequence and proteins,"},{"Start":"03:49.010 ","End":"03:53.120","Text":"and we described the link between protein sequences and biochemical information."},{"Start":"03:53.120 ","End":"03:55.520","Text":"We should understand the link between amino acid sequence and"},{"Start":"03:55.520 ","End":"04:00.060","Text":"evolutionary relationships and comprehend protein family assignment."}],"ID":29407},{"Watched":false,"Name":"Exercise 5","Duration":"3m 24s","ChapterTopicVideoID":28166,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:05.700","Text":"Hi there. Now that we\u0027ve completed the lesson on sequence and biochemical information,"},{"Start":"00:05.700 ","End":"00:08.475","Text":"we can now go into the exercises."},{"Start":"00:08.475 ","End":"00:11.910","Text":"What can the sequence of amino acids in a protein infer aside"},{"Start":"00:11.910 ","End":"00:15.690","Text":"from the protein\u0027s 3-dimensional structure and elaborate for each?"},{"Start":"00:15.690 ","End":"00:18.150","Text":"The sequence of amino acids in a protein can offer"},{"Start":"00:18.150 ","End":"00:21.015","Text":"insight into its 3-dimensional structure, its function,"},{"Start":"00:21.015 ","End":"00:23.700","Text":"cellular location, and evolution through comparisons of"},{"Start":"00:23.700 ","End":"00:27.300","Text":"the sequence with known sequences of other proteins and protein families."},{"Start":"00:27.300 ","End":"00:31.140","Text":"Protein families that have some shared structural or functional features can be"},{"Start":"00:31.140 ","End":"00:35.535","Text":"readily identified on the basis of amino acids sequence similarities,"},{"Start":"00:35.535 ","End":"00:37.560","Text":"so the sequences are looked at,"},{"Start":"00:37.560 ","End":"00:39.075","Text":"the amino acid sequences."},{"Start":"00:39.075 ","End":"00:40.880","Text":"Based on these similarities,"},{"Start":"00:40.880 ","End":"00:45.290","Text":"it can be inferred and used to look at proteins and"},{"Start":"00:45.290 ","End":"00:51.041","Text":"associate them and their similarity and function into families."},{"Start":"00:51.041 ","End":"00:55.130","Text":"The proteins are assigned to families based on the degree of similarity in"},{"Start":"00:55.130 ","End":"00:59.810","Text":"amino acid sequence when compared between the different proteins."},{"Start":"00:59.810 ","End":"01:04.745","Text":"Proteins in these families share structural and functional characteristics that again,"},{"Start":"01:04.745 ","End":"01:10.940","Text":"go back to the actual amino acid sequence and further back to the genetic sequence."},{"Start":"01:10.940 ","End":"01:15.805","Text":"Evolutionary relationships can be inferred from structural and functional similarities."},{"Start":"01:15.805 ","End":"01:17.885","Text":"This can work both ways."},{"Start":"01:17.885 ","End":"01:20.440","Text":"You see similarities, you can establish relationship,"},{"Start":"01:20.440 ","End":"01:25.160","Text":"and you can establish the evolutionary history and relationship from"},{"Start":"01:25.160 ","End":"01:30.665","Text":"the structural and functional similarities being that if you have very similar functions,"},{"Start":"01:30.665 ","End":"01:32.705","Text":"yet very different structures,"},{"Start":"01:32.705 ","End":"01:39.034","Text":"they probably have evolved separately from way back then from the common ancestor."},{"Start":"01:39.034 ","End":"01:40.595","Text":"But if you have similar function,"},{"Start":"01:40.595 ","End":"01:43.655","Text":"and similar structure, and similar sequence,"},{"Start":"01:43.655 ","End":"01:49.054","Text":"they are probably more closely related in time over evolution."},{"Start":"01:49.054 ","End":"01:54.430","Text":"Certain amino acid sequences serve as signals that determine the cellular location."},{"Start":"01:54.430 ","End":"01:58.010","Text":"Going back, what we could say is knowledge of the sequence of"},{"Start":"01:58.010 ","End":"02:02.270","Text":"amino acids in a protein can offer insight into these several things;"},{"Start":"02:02.270 ","End":"02:03.965","Text":"the structure, the function,"},{"Start":"02:03.965 ","End":"02:07.700","Text":"cellular location, and that\u0027s what we\u0027re going to talk about now, and evolution."},{"Start":"02:07.700 ","End":"02:09.760","Text":"As for cellular location,"},{"Start":"02:09.760 ","End":"02:14.000","Text":"certain amino acid sequences serve as signals that determine"},{"Start":"02:14.000 ","End":"02:19.550","Text":"the cellular location as well as chemical modification and half-life of a protein."},{"Start":"02:19.550 ","End":"02:21.980","Text":"Distinct signal sequences are used to"},{"Start":"02:21.980 ","End":"02:25.055","Text":"target certain proteins for distribution to the nucleus,"},{"Start":"02:25.055 ","End":"02:28.445","Text":"the cell surface of the cytosol and other cellular locations."},{"Start":"02:28.445 ","End":"02:31.250","Text":"It can signal for export from the cell."},{"Start":"02:31.250 ","End":"02:33.410","Text":"It can signal for directing it to"},{"Start":"02:33.410 ","End":"02:36.680","Text":"the nucleus and it\u0027s been established over comparison of"},{"Start":"02:36.680 ","End":"02:42.505","Text":"sequences and seeing certain proteins that are found in the nucleus versus the cytoplasm."},{"Start":"02:42.505 ","End":"02:46.190","Text":"This location is associated with a specific sequence"},{"Start":"02:46.190 ","End":"02:50.180","Text":"that is found in the amino acid chain."},{"Start":"02:50.180 ","End":"02:54.470","Text":"From this, we can take home the message that the amino acid sequence,"},{"Start":"02:54.470 ","End":"02:58.220","Text":"while flexible and variable,"},{"Start":"02:58.220 ","End":"03:05.510","Text":"has a significant role and is linked to many things like location,"},{"Start":"03:05.510 ","End":"03:08.390","Text":"function, structure, et cetera."},{"Start":"03:08.390 ","End":"03:13.595","Text":"Which is why so many biochemists and other type of molecular biologists"},{"Start":"03:13.595 ","End":"03:19.520","Text":"study and look at these sequences to have a better understanding of organisms,"},{"Start":"03:19.520 ","End":"03:24.330","Text":"functions, proteins, processes, et cetera."}],"ID":29408},{"Watched":false,"Name":"Exercise 6","Duration":"46s","ChapterTopicVideoID":28167,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:04.682","Text":"We\u0027ve been talking about sequence and biochemical information."},{"Start":"00:04.682 ","End":"00:06.689","Text":"Let\u0027s dive into the exercise."},{"Start":"00:06.689 ","End":"00:10.425","Text":"What criteria is used to assign proteins to families?"},{"Start":"00:10.425 ","End":"00:12.840","Text":"Proteins are assigned to families based on the degree of"},{"Start":"00:12.840 ","End":"00:15.405","Text":"similarity in amino acid sequence."},{"Start":"00:15.405 ","End":"00:20.160","Text":"Members of a family are identical across 25 percent or more of their sequences,"},{"Start":"00:20.160 ","End":"00:24.125","Text":"so when you look at different proteins within the same family,"},{"Start":"00:24.125 ","End":"00:28.850","Text":"you\u0027ll see 25 percent or more identity between their sequences."},{"Start":"00:28.850 ","End":"00:31.580","Text":"Proteins in these families usually share"},{"Start":"00:31.580 ","End":"00:34.850","Text":"at least some structural and functional characteristics."},{"Start":"00:34.850 ","End":"00:37.280","Text":"Some families are defined however,"},{"Start":"00:37.280 ","End":"00:40.820","Text":"by identities involving only a few amino acid residues that"},{"Start":"00:40.820 ","End":"00:45.450","Text":"are critical to a certain function within some families."}],"ID":29409},{"Watched":false,"Name":"Exercise 7","Duration":"1m 36s","ChapterTopicVideoID":28168,"CourseChapterTopicPlaylistID":277600,"HasSubtitles":true,"ThumbnailPath":null,"UploadDate":null,"DurationForVideoObject":null,"Description":null,"MetaTitle":null,"MetaDescription":null,"Canonical":null,"VideoComments":[],"Subtitles":[{"Start":"00:00.000 ","End":"00:02.610","Text":"We\u0027ve been talking about sequence and"},{"Start":"00:02.610 ","End":"00:06.360","Text":"biochemical Information within the chapter of amino acids,"},{"Start":"00:06.360 ","End":"00:09.195","Text":"peptides, and proteins. Let\u0027s test our knowledge."},{"Start":"00:09.195 ","End":"00:12.270","Text":"If we sum up the knowledge accumulated thus far,"},{"Start":"00:12.270 ","End":"00:15.240","Text":"what can be said about what the string of letters denoting"},{"Start":"00:15.240 ","End":"00:19.290","Text":"the amino acid sequence of a given protein elucidates?"},{"Start":"00:19.290 ","End":"00:21.330","Text":"Let\u0027s try to simplify this."},{"Start":"00:21.330 ","End":"00:24.480","Text":"The simple string of letters denoting the amino acid sequence of"},{"Start":"00:24.480 ","End":"00:29.040","Text":"a particular protein indicates its 3-dimensional structure."},{"Start":"00:29.040 ","End":"00:31.680","Text":"The letters denoting the amino acid sequence,"},{"Start":"00:31.680 ","End":"00:35.310","Text":"this sequence of valine, leucine,"},{"Start":"00:35.310 ","End":"00:38.460","Text":"arginine, asparagine, how they are linked"},{"Start":"00:38.460 ","End":"00:42.090","Text":"and ordered affects its 3-dimensional structure."},{"Start":"00:42.090 ","End":"00:48.530","Text":"Furthermore, it shows how life evolved on this planet because it gives us a clue when"},{"Start":"00:48.530 ","End":"00:51.710","Text":"looking at similar function and"},{"Start":"00:51.710 ","End":"00:55.040","Text":"organisms that are either distantly related or closely related,"},{"Start":"00:55.040 ","End":"01:01.010","Text":"we will see that represented in similarity in sequence or difference in sequence,"},{"Start":"01:01.010 ","End":"01:03.800","Text":"or if you\u0027re looking at the global protein sequence,"},{"Start":"01:03.800 ","End":"01:07.280","Text":"the entire gene coding for that protein,"},{"Start":"01:07.280 ","End":"01:11.000","Text":"you\u0027ll see at least some portion that remains the same even between"},{"Start":"01:11.000 ","End":"01:14.900","Text":"very distant organisms that the whole gene seems very different,"},{"Start":"01:14.900 ","End":"01:16.460","Text":"the whole sequence between the 2."},{"Start":"01:16.460 ","End":"01:19.205","Text":"But there may be some similarity,"},{"Start":"01:19.205 ","End":"01:21.620","Text":"some ratio in some part of that."},{"Start":"01:21.620 ","End":"01:27.440","Text":"This whole idea of sequence related to protein, related to structure,"},{"Start":"01:27.440 ","End":"01:31.010","Text":"related to function also allows us to figure"},{"Start":"01:31.010 ","End":"01:36.360","Text":"out evolution on this planet of different organisms."}],"ID":29410}],"Thumbnail":null,"ID":277600}]

[{"ID":272566,"Videos":[28485,28486,28487,28488,28489,28490,28491,28492,28493,28494,28495,28496,28497]},{"ID":277599,"Videos":[29393,29394,29395,29396,29397,29398,29399,29400,29388,29389,29390,29391,29392]},{"ID":277600,"Videos":[29401,29402,29403,29404,29405,29406,29407,29408,29409,29410]}];

[29393,29394,29395,29396,29397,29398,29399,29400,29388,29389,29390,29391,29392];

1

15