Week 1 Proteomics Live Session

01:50:13
https://www.youtube.com/watch?v=bNKTw4YBJEA

Zusammenfassung

TLDRLa session live de la première semaine du cours sur la protéomique introduit les étudiants au concept de protéomique, qui est l'étude complète des protéines présentes dans un organisme. Elle couvre les acides aminés, leurs structures (primaires, secondaires, tertiaires et quaternaires), et les méthodes telles que la spectrométrie pour comprendre leur concentration et leur rôle dans la santé. Les discussions incluent l'importance des angles phi et psi, le repliement des protéines selon le paradoxe de Levinthal, et le rôle des chaperons dans le repliement correct. Anfinsen's experiment est évoqué pour illustrer comment la structure et fonction des protéines sont liées et peuvent être restaurées après dénaturation. Le cours met aussi en lumière les défis de l'identification et de la quantification des protéines dans un contexte de maladies.

Mitbringsel

  • 📅 Cours de 8 semaines couvrant la protéomique et ses concepts.
  • 🔍 Focus sur l'étude des protéines dans les cellules et organismes.
  • 🧬 Importance des acides aminés et de la structure protéique.
  • 📊 Utilisation de techniques pour mesurer la concentration protéique.
  • 🧪 Role de la spectrométrie et des méthodes analytiques.
  • 💬 Discussion des doutes et questions des étudiants.
  • 🧩 Le repliement correct des protéines est essentiel pour leur fonction.
  • 🔄 Les mutés peuvent entraîner des dysfonctionnements.
  • 🔬 Techniques protéomiques avancées pour la recherche biomédicale.
  • 📚 Opportunité d'apprentissage interactif pour les étudiants.

Zeitleiste

  • 00:00:00 - 00:05:00

    Bienvenue au cours d'introduction à Proix. Cette séance en direct de la première semaine couvre les concepts théoriques qui seront explorés au cours des huit semaines. Les étudiants sont encouragés à partager leurs idées sur ce qu'ils comprennent de Proix après avoir suivi les premières leçons.

  • 00:05:00 - 00:10:00

    La discussion se concentre sur le terme 'omique', qui signifie l'ensemble complet des protéines présentes dans un organisme. Ce cours abordera l'évolution des techniques pour comprendre l'expression des protéines, leur corrélation avec des maladies et l'importance des protéines dans la biologie cellulaire.

  • 00:10:00 - 00:15:00

    Le cours aborde des concepts de base sur les acides aminés, leurs rôles comme blocs de construction des protéines, leurs divers groupes R, et la complexité qu'ils apportent aux structures et fonctions biologiques.

  • 00:15:00 - 00:20:00

    Les lois de Beer-Lambert sont introduites pour discuter de la mesure de l'absorbance et de son importance dans la détermination des concentrations d'inconnues par absorbance, ainsi que les caractéristiques spécifiques des acides aminés aromatiques qui absorbent à 280 nm grâce à leurs structures en anneau conjugué.

  • 00:20:00 - 00:25:00

    La discussion couvre le concept d'absorbance des acides aminés aromatiques, en mettant en avant que les structures en anneau conjugué permettent une absorption stable due aux électrons P délocalisés.

  • 00:25:00 - 00:30:00

    Les acides aminés essentiels et non essentiels sont discutés, mettant en évidence ceux que le corps ne peut pas synthétiser et qui doivent être obtenus par l'alimentation. L'importance des acides aminés pour les processus biologiques et leur disponibilité à travers l'alimentation sont soulignées.

  • 00:30:00 - 00:35:00

    Le concept de chiralité est abordé, ainsi que les configurations L et D des acides aminés. Les aminoacides L sont dominants dans les protéines humaines, et la possibilité que des acides aminés D soient présents dans d'autres organismes comme les bactéries est suggérée pour un examen ultérieur.

  • 00:35:00 - 00:40:00

    La stéréoconfiguration des acides aminés est expliquée en termes de règles de priorité et d’arrangement spatial, avec l’introduction des nomenclatures R et S fondées sur les numéros atomiques.

  • 00:40:00 - 00:45:00

    L'ionisation des acides aminés est discutée, avec une explication des Zwitterions et comment les différents niveaux de pH peuvent favoriser des formes cationiques ou anioniques.

  • 00:45:00 - 00:50:00

    La technique SDS-PAGE est mentionnée comme application basée sur les propriétés des Zwitterions, illustrant comment les acides aminés se déplacent dans un champ électrique en fonction de leur charge nette à différents pH.

  • 00:50:00 - 00:55:00

    La formation des protéines est reliée aux liaisons peptidiques et aux réactions de condensation. Des explications sur les caractéristiques des liaisons peptidiques, leurs résistances et comment elles sont hydrolysées sont données.

  • 00:55:00 - 01:00:00

    La rigidité des liaisons peptidiques est due à leur caractère de résonance partielle à double liaison, contribuant à la stabilité structurelle des protéines. Les concepts de hybridation et de configuration planaire sont expliqués.

  • 01:00:00 - 01:05:00

    Les angles phi et psi permettent la rotation libre dans les chaînes polypeptidiques, influençant les structures secondaires des protéines, un aspect central des modèles en cartes de Ramachandran pour l'analyse stéréochimique.

  • 01:05:00 - 01:10:00

    Différenciation des structures secondaires, alpha-hélice et feuillet bêta, en utilisant les angles phi et psi. Les stabilités et les types de liaisons, ainsi que le rôle de l’hélice alpha dans le repliement des protéines sont examinés.

  • 01:10:00 - 01:15:00

    Les structures tertiaires des protéines se forment par des interactions entre les résidus et le squelette, stabilisées par diverses forces et liaisons. Le rôle des groupes hydrophobes et des interactions ioniques est crucial pour la structure 3D.

  • 01:15:00 - 01:20:00

    L'importance des structures tertiaires et quaternaires dans la formation biologique fonctionnelle des protéines, ainsi que les interactions stabilisatrices et le rôle crucial des chaperons pour le repliement correct sont soulignés.

  • 01:20:00 - 01:25:00

    La discussion de l'expérience d'Anfinsen sur le repliement des protéines démontre que l'information de repliement se trouve dans la séquence d'acides aminés et montre l'importance du retour à la structure native pour la fonctionnalité biologique.

  • 01:25:00 - 01:30:00

    L'efficacité du repliement des protéines est abordée via le paradoxe de Levinthal et les paysages énergétiques, expliquant comment les protéines atteignent rapidement leurs états natifs malgré un vaste nombre de conformations possibles.

  • 01:30:00 - 01:35:00

    Le concept de structures quaternaires est présenté, expliquant comment plusieurs sous-unités protéiques interagissent pour former des complexes fonctionnels, avec leurs implications biologiques et évolutives.

  • 01:35:00 - 01:40:00

    Les technologies omiques, telles que la protéomique et la génomique, sont discutées pour leur rôle dans la compréhension des fonctions biologiques des protéines à partir de l'ensemble du génome, de l'expression des gènes et de la variabilité des métabolites.

  • 01:40:00 - 01:50:13

    Clôture du cours avec une vue d'ensemble sur l'importance de la compréhension des protéines à travers la protéomique et comment des techniques comme la protéogénomique peuvent fournir une vue intégrée des fonctions biologiques et des maladies.

Mehr anzeigen

Mind Map

Mind Map

Häufig gestellte Fragen

  • Qu'est-ce que la protéomique ?

    La protéomique est l'étude de l'ensemble des protéines présentes dans un organisme, explorant notamment leur expression et rôle dans différentes conditions biologiques.

  • Pourquoi étudier la protéomique ?

    L'étude de la protéomique est importante pour comprendre les mécanismes biologiques et les implications des protéines dans les maladies et le développement de thérapies.

  • Comment mesure-t-on la concentration inconnue d'une protéine en solution ?

    On calcule cette concentration en utilisant une courbe standard et la loi de Beer-Lambert qui relie l'absorbance d'une solution à sa concentration.

  • Pourquoi les acides aminés aromatiques absorbent-ils à 280 nm ?

    Les acides aminés aromatiques, en raison de leurs structures cycliques, ont une absorption à 280 nm qui est caractéristique des protéines.

  • Quelles sont les principales structures secondaires des protéines ?

    La structure secondaire des protéines comprend essentiellement les hélices alpha et les feuillets bêta qui sont stabilisés par des liaisons hydrogène.

  • Quelle est l'importance des angles phi et psi dans les protéines ?

    Ces angles sont importants car ils influencent la conformation d'une protéine et peuvent restreindre ou permettre certaines structures.

  • Comment se forme la structure tertiaire d'une protéine ?

    Les interactions telles que les liaisons hydrogène et les interactions hydrophobes façonnent la structure tertiaire des protéines, déterminant leur fonction biologique.

  • Comment les protéines parviennent-elles à un repliement rapide et efficace ?

    Les protéines se replient rapidement grâce à des paysages énergétiques qui guident les transitions vers des états stables, selon le paradoxe de Levinthal.

  • Quel est l'effet des mutations sur la structure des protéines ?

    Ces changements peuvent altérer la fonction d'une protéine et provoquer des maladies génétiques et des dysfonctionnements pathologiques.

  • Que sont les protéases et leur rôle dans l'étude des protéines ?

    Ce sont des enzymes qui clivent les protéines à des sites spécifiques, aidant ainsi à la digestion ou l'analyse des protéines.

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Untertitel
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Automatisches Blättern:
  • 00:00:02
    welcome to the course of introduction to
  • 00:00:06
    proix uh so this is the week one uh live
  • 00:00:10
    session so what we will do in this uh
  • 00:00:13
    eight week so since you know that this
  • 00:00:15
    is
  • 00:00:17
    a 8 week course so what we will do is
  • 00:00:20
    that in this span of 8 weeks uh we will
  • 00:00:22
    be going through
  • 00:00:25
    different uh theories Concepts that you
  • 00:00:27
    have already are studying in the through
  • 00:00:30
    the videos then we will do some uh
  • 00:00:33
    problems and also we will try to do some
  • 00:00:36
    Hands-On which will be extra uh to
  • 00:00:39
    whatever is being there in the syllabus
  • 00:00:42
    as per the time permit so before uh
  • 00:00:46
    starting uh today's uh session so first
  • 00:00:49
    of all uh if you all can tell me briefly
  • 00:00:54
    that uh what are your uh so we'll come
  • 00:00:58
    I'll come to your uh doubts so before
  • 00:01:01
    that if you all can tell me briefly what
  • 00:01:04
    is your idea about protom miix and after
  • 00:01:07
    going through the first uh lecture what
  • 00:01:09
    you uh what do you feel proix is about
  • 00:01:12
    anyone would like to say and then we
  • 00:01:16
    will go on with your doubts and then we
  • 00:01:18
    will look at the different uh revisit
  • 00:01:21
    the different concepts and we will try
  • 00:01:24
    to make it interactive because uh in
  • 00:01:26
    your uh video I think you are listening
  • 00:01:30
    and then you are writing in the query
  • 00:01:32
    but here you are getting an opportunity
  • 00:01:35
    uh to interact directly uh so it would
  • 00:01:38
    be good so if anyone can tell that uh if
  • 00:01:42
    there was any idea beforehand uh
  • 00:01:45
    regarding proix or is first time uh uh
  • 00:01:49
    you are doing and what is your what was
  • 00:01:50
    your idea and uh and what is the change
  • 00:01:55
    in any idea or you what uh to the same
  • 00:01:59
    and what was the what is what was your
  • 00:02:01
    main idea behind taking this course
  • 00:02:04
    anyone would like to
  • 00:02:11
    comment what do you mean by this term
  • 00:02:13
    Pro
  • 00:02:24
    anyone so shall I call by name
  • 00:02:30
    okay so okay so if you so if I give my
  • 00:02:33
    introduction so that would make
  • 00:02:35
    everything real so I am anit who is in
  • 00:02:38
    currently in final year of PhD mte PhD
  • 00:02:42
    12 degree from it Bombay uh so I am a PM
  • 00:02:46
    fellow and I'm taking this uh so you can
  • 00:02:48
    also if you want you can also introduce
  • 00:02:50
    and interact so for example for instance
  • 00:02:53
    if you can tell about why what is what
  • 00:02:57
    was your idea behind to taking this and
  • 00:03:01
    uh what do you think of the term prot
  • 00:03:14
    me
  • 00:03:17
    sorry if you come
  • 00:03:20
    again stud
  • 00:03:24
    of protein folding
  • 00:03:31
    protein
  • 00:03:34
    structur
  • 00:03:35
    okay I think Puja has raised her hand
  • 00:03:39
    yes if you can go
  • 00:03:43
    through stud of
  • 00:03:51
    proteins okay study of proteins uh so if
  • 00:03:55
    we break down the
  • 00:03:57
    term yes uh uh soam I guess
  • 00:04:04
    yes
  • 00:04:06
    mhm so what is the meaning of
  • 00:04:18
    protome set of
  • 00:04:20
    protein okay so the term if I say if
  • 00:04:24
    anyone would like to try anyone else
  • 00:04:26
    would like to try
  • 00:04:33
    anyone Mary
  • 00:04:39
    or Katia Priya
  • 00:04:49
    anyone IA
  • 00:04:53
    tanishka okay
  • 00:04:56
    so so you have uh got almost so proteom
  • 00:05:00
    so the term om yes anyone was
  • 00:05:06
    saying so we we say that omix it comes
  • 00:05:09
    from om right so that is means all so
  • 00:05:13
    proteo refers to the set of proteins
  • 00:05:15
    that each and every protein that is
  • 00:05:17
    present in an individual in a Cell uh in
  • 00:05:21
    an individual it an organ it an organism
  • 00:05:24
    so you can say organal proteum cellular
  • 00:05:28
    proteo okay so from where the term comes
  • 00:05:30
    of proteomic so here in this course you
  • 00:05:33
    will be you are learning about some
  • 00:05:36
    basic protein science I think that is
  • 00:05:37
    covered in this week one and next to
  • 00:05:40
    study about the proteins all proteins so
  • 00:05:42
    for that we need to understand if we try
  • 00:05:45
    to understand the protein expression of
  • 00:05:47
    the cell which we will see then we need
  • 00:05:50
    to do many techniques from where we can
  • 00:05:53
    identify and understand the expression
  • 00:05:55
    level of the proteins and then
  • 00:05:57
    understand and correlate in the disease
  • 00:05:59
    St so this is exactly the idea behind
  • 00:06:03
    proteo mix okay so which is the entire
  • 00:06:05
    set of studying of the entire set of
  • 00:06:07
    proteins not individual proteins or
  • 00:06:10
    subset of proteins rather the entire
  • 00:06:12
    proteins and then in this course we will
  • 00:06:15
    be going through that how the field has
  • 00:06:18
    evolved how different techniques have
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    evolved and how it is still rapidly
  • 00:06:22
    evolving and progressing for
  • 00:06:25
    understanding of the proteins at
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    different level at different states uh
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    ptms all these comes under proteins
  • 00:06:33
    proteomics okay so but uh before I uh
  • 00:06:38
    going to that I I I also wanted to
  • 00:06:41
    revisit some Concepts before that uh uh
  • 00:06:44
    would anyone would like to tell that by
  • 00:06:46
    going through this uh week's lecture or
  • 00:06:49
    videos have you found any doubt or do
  • 00:06:51
    you have any doubt that I need to
  • 00:06:53
    discuss it specifically uh before uh
  • 00:06:56
    going into uh the discussion
  • 00:07:01
    do you have all any pressing doubt or
  • 00:07:03
    query regarding the course or regarding
  • 00:07:06
    uh that particular question particular
  • 00:07:08
    concept particular
  • 00:07:12
    thing
  • 00:07:15
    no yes
  • 00:07:29
    yes guanidium chloride can also be used
  • 00:07:32
    I am I will uh come to that concept as
  • 00:07:35
    well in my uh to the presentation I will
  • 00:07:40
    come to yes gu cide is also used uh that
  • 00:07:44
    is also a denaturing
  • 00:07:47
    agent
  • 00:07:49
    yes okay so I think then we can go step
  • 00:07:52
    by step uh go is topic by topic and if
  • 00:07:55
    you find out anything difficulty while
  • 00:07:57
    you are going through the video and want
  • 00:08:00
    to clarify then definitely you
  • 00:08:03
    can uh talk to me and ask and as I said
  • 00:08:08
    that today since in this week uh there
  • 00:08:11
    was uh not much uh possibility of having
  • 00:08:16
    Hands-On sessions but as we go along
  • 00:08:18
    with the course we will be having
  • 00:08:19
    Hands-On here in the uh sessions as well
  • 00:08:23
    okay so that uh whatever is being taught
  • 00:08:26
    in the lectures and whatever assignments
  • 00:08:29
    you are doing along with that you get
  • 00:08:30
    some extra exposure as well okay so I
  • 00:08:34
    will now go to the presentation and in
  • 00:08:37
    each topic you are free to ask any time
  • 00:08:41
    any query you have might be it will be
  • 00:08:44
    difficult for me to follow in the chat
  • 00:08:45
    because in the full screen version uh I
  • 00:08:49
    cannot see yes uh Nisha I guess okay it
  • 00:08:53
    was my mistake uh so in the chat it
  • 00:08:55
    becomes difficult to follow uh because
  • 00:08:58
    uh in the present mode generally I am
  • 00:09:01
    not able to see the screen uh but
  • 00:09:05
    definitely uh you can stop interrupt and
  • 00:09:08
    unmute and ask and feel free to ask and
  • 00:09:11
    make it as much interactive as possible
  • 00:09:14
    uh you are free to ask any question
  • 00:09:18
    okay yeah so I will just start with some
  • 00:09:22
    of the concept yeah and if I ask also
  • 00:09:27
    questions so if you uh please feel free
  • 00:09:30
    to respond and the way the more
  • 00:09:33
    interactive we will make the more we
  • 00:09:35
    will learn it together okay so I'm
  • 00:09:36
    requesting everyone to just be
  • 00:09:38
    interactive and be answerable to
  • 00:09:41
    whatever uh whichever answers you know
  • 00:09:43
    as well as whichever you don't know and
  • 00:09:45
    you have any doubt like just now so did
  • 00:09:48
    so everyone is encouraged to do the same
  • 00:09:52
    okay so we are going uh basic starting
  • 00:09:56
    from the basic scratch basic
  • 00:09:58
    biochemistry
  • 00:09:59
    the introduction to amino acids right so
  • 00:10:03
    I think all of you are well aware about
  • 00:10:06
    the concept of amino acids is there
  • 00:10:08
    anyone who uh who doesn't know in depth
  • 00:10:13
    about amino
  • 00:10:15
    acids I guess no uh so it is the
  • 00:10:19
    building blocks of proteins and we know
  • 00:10:21
    that the amino acid are different 20
  • 00:10:24
    types of amino acids uh most popular
  • 00:10:27
    ones as well as the 21st second amino
  • 00:10:30
    acids are also being identified and in
  • 00:10:33
    course of time it might be we can see
  • 00:10:35
    that there are different types of amino
  • 00:10:37
    acids right so firstly there are a major
  • 00:10:41
    thing that comes into uh play or action
  • 00:10:45
    is that the uh what is
  • 00:10:50
    the so just a minute I'll
  • 00:10:56
    check so the major thing that I wanted
  • 00:11:00
    to say is that there are different R
  • 00:11:02
    groups that makes it diverse as you know
  • 00:11:06
    so there will be aliphatic art groups
  • 00:11:09
    uncharged art groups positively charged
  • 00:11:11
    art groups negatively charged art groups
  • 00:11:13
    aromatic art groups so all these makes
  • 00:11:16
    the the backbone is same with the nh2
  • 00:11:21
    and the amine and the co carox B carox
  • 00:11:27
    Lions but the whatever the change in the
  • 00:11:30
    type of the art chain Branch chain or
  • 00:11:35
    Branch it can be positive it can be
  • 00:11:37
    negatively charged so all this leads to
  • 00:11:39
    the different forms of amino acids right
  • 00:11:41
    so this uh is what from there the
  • 00:11:44
    complexity starts and from where the
  • 00:11:48
    field of the concept the proteins build
  • 00:11:51
    up which makes up all our muscles
  • 00:11:53
    tissues organs and then finally the
  • 00:11:57
    diversity the whatever changes that is
  • 00:12:00
    visible to each one of us is visible
  • 00:12:04
    because of the changes in this proteins
  • 00:12:06
    so you know that uh in the genomics
  • 00:12:10
    after you do if you do a uh gen
  • 00:12:12
    sequencing between me you or any animal
  • 00:12:17
    if you take chimpanzee or a monkey the
  • 00:12:21
    genetic sequence of the gene sequence
  • 00:12:23
    will be or the DNA sequence will be
  • 00:12:25
    roughly 99% similar but still we all are
  • 00:12:28
    very much different and the reason for
  • 00:12:31
    it is nothing but only the proteins the
  • 00:12:34
    way amino acids are done or the way
  • 00:12:37
    amino acids are developed the the
  • 00:12:40
    proteins are there different forms of
  • 00:12:42
    proteins and Performing different
  • 00:12:44
    structure and function then there comes
  • 00:12:47
    definitely the concept of the
  • 00:12:50
    alternative splicing and all where
  • 00:12:52
    different proteins are formed due
  • 00:12:55
    to make up different structures
  • 00:12:58
    different function so all these are very
  • 00:13:01
    much required to for the field of uh so
  • 00:13:08
    in this to make the things diverse and
  • 00:13:10
    each and every individual to be
  • 00:13:12
    different performing different functions
  • 00:13:14
    so all these are very much
  • 00:13:17
    crucial so now if
  • 00:13:22
    we move ahead so these are basically the
  • 00:13:26
    amino acid structures so different
  • 00:13:29
    structure so here if we can say that the
  • 00:13:31
    glycine which is very small and have
  • 00:13:34
    only H so the most simplest form of
  • 00:13:38
    amino acid is glycin of course you all
  • 00:13:41
    must be aware of it which doesn't
  • 00:13:43
    contain any in the only H in the fourth
  • 00:13:48
    uh chain then com ch3 alanine which is
  • 00:13:51
    again just the complex version of
  • 00:13:54
    glycine which contains ch3 then we have
  • 00:13:58
    the serin tronin cine of the
  • 00:14:00
    nucleophilic then you have the
  • 00:14:02
    hydrophobic ones which is the branch and
  • 00:14:04
    amino acids valine Lucine isoline
  • 00:14:07
    methionine Proline then you have the
  • 00:14:09
    aromatic amino acids like phon tyosin
  • 00:14:12
    cryopen acidic amino acid like aspartic
  • 00:14:14
    acid glutamic acid and asparagin
  • 00:14:17
    glutamine and the basic like hisin Li in
  • 00:14:19
    arine among which the aromatic amino
  • 00:14:22
    acids and Proline uh play a crucial role
  • 00:14:26
    because of its bulky nature and it
  • 00:14:30
    uh it imparts a different functional and
  • 00:14:34
    uh structural uh properties to a
  • 00:14:36
    particular protein so specifically uh
  • 00:14:39
    Proline is of great interest to
  • 00:14:42
    study so now in the BL lbert law before
  • 00:14:46
    going on so how many of you are aware
  • 00:14:49
    about BL lber
  • 00:14:52
    law so who will be uh telling about BL
  • 00:14:56
    lers law
  • 00:14:59
    so you all are uh studying in colleges
  • 00:15:02
    right so they are you are familiar with
  • 00:15:06
    it so how many of you are familiar and
  • 00:15:09
    have heard about BL lers SL please raise
  • 00:15:11
    your
  • 00:15:15
    hand okay one har and the others are not
  • 00:15:18
    aware about BL numers
  • 00:15:24
    law you all have Puja yes others
  • 00:15:31
    yeah
  • 00:15:34
    yes so so who would like to say Puja you
  • 00:15:39
    can go or prya what is what do you what
  • 00:15:42
    is BL Numbers Law
  • 00:16:01
    the absorbance is directly proportional
  • 00:16:03
    to concentration
  • 00:16:06
    and
  • 00:16:09
    yes and the end of the pathway of the
  • 00:16:12
    light right so yeah so before going into
  • 00:16:17
    that uh concept
  • 00:16:19
    of what told so before that we need to
  • 00:16:22
    have understanding what is the incidence
  • 00:16:25
    what is the transmittance what is the
  • 00:16:26
    absorbance so what is the meaning of the
  • 00:16:28
    word absor absorbance if I say if as you
  • 00:16:31
    said that absorbance is directly
  • 00:16:33
    proportional to the uh concentration and
  • 00:16:36
    length so
  • 00:16:38
    the application lies is that in that
  • 00:16:41
    absorbance is directly proportional to
  • 00:16:43
    concentration so that we can measure the
  • 00:16:45
    unknown concentration of a particular
  • 00:16:47
    solution so that's why BL lbert law is
  • 00:16:50
    used and I think you all have done an
  • 00:16:52
    experiment where have you have used and
  • 00:16:55
    uh absorbance have measured uh the
  • 00:16:59
    absorbance and Tred to find out the
  • 00:17:01
    concentration unknown concentration of a
  • 00:17:03
    particular sample which we don't know so
  • 00:17:06
    from a standard graph so if we know the
  • 00:17:09
    absorbance of a standard concentrations
  • 00:17:12
    of a graph of a solution then from a
  • 00:17:15
    graph if we make a particular equation
  • 00:17:19
    and if we can draw uh derive an equation
  • 00:17:22
    then from for that an unknown
  • 00:17:24
    concentration can easily be calculated
  • 00:17:27
    but before going into to that so what is
  • 00:17:30
    from where the term absorbance is coming
  • 00:17:32
    so firstly is the transmittance so in
  • 00:17:35
    this particular for instance in this
  • 00:17:37
    particular cuate if we have the solution
  • 00:17:40
    and if we are inciting a light then and
  • 00:17:44
    it will be finally after getting
  • 00:17:46
    absorbed deflected reflected all these
  • 00:17:49
    things it will be
  • 00:17:50
    transmitted right so this comes the
  • 00:17:53
    concept of transmittance which is the
  • 00:17:55
    transmitted light upon the incident
  • 00:17:58
    light
  • 00:17:59
    T = to I by I that what was the initial
  • 00:18:03
    incident light
  • 00:18:06
    provided which was and in the numerator
  • 00:18:09
    be the what is the transmitted light so
  • 00:18:12
    the percentage is t% will be I by I into
  • 00:18:16
    100 now absorbance is the negative
  • 00:18:20
    logarithmic of transmittance okay so
  • 00:18:23
    what is absorbance absorbance is nothing
  • 00:18:26
    but the negative logarithmic of the
  • 00:18:29
    transmittance or log 10 i0 by I so zero
  • 00:18:33
    absorbance corresponds to 100%
  • 00:18:36
    transmittance so zero absorbance
  • 00:18:40
    corresponds to our 100% transmittance
  • 00:18:43
    And Vic Versa is that 100% absorbance
  • 00:18:47
    means there will be no transmit it will
  • 00:18:49
    be finally fully absorbed right so as
  • 00:18:52
    you
  • 00:18:52
    mentioned AAL to epon CL so this Epsilon
  • 00:18:58
    is the absorption coefficient and the
  • 00:19:01
    major thing that has been used is used
  • 00:19:03
    extensively in our biological studies
  • 00:19:05
    and research is to find the unknown
  • 00:19:08
    concentration for the absorbance now
  • 00:19:11
    this is where uh it helps us in getting
  • 00:19:15
    particular things so you can see that
  • 00:19:17
    for 38 microl there will be a certain
  • 00:19:19
    absorbance and for a 152 microl there
  • 00:19:22
    will be a certain state of absorbance so
  • 00:19:25
    absorbance increases quite old time
  • 00:19:28
    times when there is an increase in
  • 00:19:30
    concentration so in this way if we if we
  • 00:19:33
    can measure if we know for example five
  • 00:19:36
    or six data points we know that this
  • 00:19:40
    concentration this is the known
  • 00:19:42
    concentration we made a standard curve
  • 00:19:45
    we uh get to measure the absorbance for
  • 00:19:48
    each of these five and six uh
  • 00:19:51
    particular concentration absorbance then
  • 00:19:54
    the seventh or seventh concentration
  • 00:19:56
    that would be the unknown concentration
  • 00:19:59
    uh we can derive from this straight line
  • 00:20:02
    from this equation so sorry so from this
  • 00:20:06
    equation we can get to measure the
  • 00:20:09
    absorbance okay so this is a standard
  • 00:20:12
    curve we can say and from here for the
  • 00:20:15
    seventh unknown concentration we can
  • 00:20:17
    easily so if we can get the absorbance
  • 00:20:20
    so how it is generally done so I hope
  • 00:20:24
    that you everyone of you know for
  • 00:20:26
    example this is an unknown concentration
  • 00:20:28
    graph where you will be getting so there
  • 00:20:31
    are 1 2 3 4 5 six data points but the
  • 00:20:34
    seventh data point the absorbance comes
  • 00:20:36
    something around here right if the
  • 00:20:39
    absorbance comes here so we need to
  • 00:20:43
    extend the line to the place where it is
  • 00:20:47
    reaching and then we need to draw the uh
  • 00:20:50
    draw the straight line and whatever
  • 00:20:52
    concentration it comes so that is a
  • 00:20:55
    particular concentration of that unknown
  • 00:20:58
    sample with absorbance for instance 1.3
  • 00:21:01
    so for 1.3 absorbance we will draw the
  • 00:21:04
    line and draw the and get the
  • 00:21:07
    concentration so am I right so I think
  • 00:21:10
    all of you uh know about this but still
  • 00:21:13
    I stressed out on the fact now tell me
  • 00:21:16
    that what is the absorbance of
  • 00:21:19
    cryptopanic so what is the absorbance of
  • 00:21:25
    cryptopanic amino acid mostly it is
  • 00:21:28
    considered so you can tell about Crypt
  • 00:21:30
    fan I think this is
  • 00:21:35
    uh 28 nanometer so all agree with
  • 00:21:40
    it who all agree just raise your hand
  • 00:21:43
    with 280
  • 00:21:45
    nanometer okay okay
  • 00:21:51
    others
  • 00:21:57
    Okay so your voice is not clear but I
  • 00:22:00
    could understand that you were saying
  • 00:22:01
    270 something are you telling like
  • 00:22:05
    that okay okay so this is in which
  • 00:22:12
    range 280 nanometers or 270 something
  • 00:22:15
    like was mentioning what is the
  • 00:22:21
    range so will you tell me now krytan is
  • 00:22:25
    absorbing at 280
  • 00:22:27
    nanometer does glycine or alanine what
  • 00:22:30
    is their
  • 00:22:36
    absorbance
  • 00:22:39
    anyone for glycin
  • 00:22:49
    absorbance alanin absorbance anyone
  • 00:22:51
    would like to try
  • 00:22:55
    yes yes uh Vil
  • 00:23:01
    anyone can
  • 00:23:02
    try do you think that the absorbance by
  • 00:23:05
    Krypt 280 nanom all the amino acids will
  • 00:23:08
    have the same absorbance because each
  • 00:23:10
    and everyone is amino acid what are your
  • 00:23:13
    take Let's uh
  • 00:23:15
    discuss for instance we don't know what
  • 00:23:18
    do you
  • 00:23:20
    feel that
  • 00:23:27
    yes only aromatic Amis will show so any
  • 00:23:31
    particular reason for
  • 00:23:43
    that aromaticity is a property but what
  • 00:23:48
    is aromatic ring is there uh so then
  • 00:24:00
    okay so aromatic the aromatic communes
  • 00:24:03
    will have arom okay so you have tried
  • 00:24:05
    others can would they like to extend
  • 00:24:10
    yes uh
  • 00:24:17
    your I could not hear you
  • 00:24:20
    sorry as anyone able to hear
  • 00:24:23
    then you can write in chat box now I can
  • 00:24:26
    see
  • 00:24:34
    five months right yeah yeah so that is
  • 00:24:38
    the actual thing so we will see now
  • 00:24:43
    why yeah so aromatic amus is absorbed at
  • 00:24:47
    280 nanometer why because they have this
  • 00:24:50
    conjugated ring structure so what har
  • 00:24:53
    has mentioned it correct and what P was
  • 00:24:56
    trying to intend to say that yes it is
  • 00:24:59
    an aromatic uh ring which gives it a
  • 00:25:03
    property but actual reason is that it
  • 00:25:06
    has the conjugated Pi bonds okay so
  • 00:25:10
    these Pi bonds are Delo are in a
  • 00:25:14
    delocalized state and not in a very
  • 00:25:17
    localized or confirm state so what
  • 00:25:19
    happens is that whenever an ubite is
  • 00:25:22
    passing through it and if one molecule
  • 00:25:25
    gets absorbed to it so the electrons so
  • 00:25:27
    what is the basic fundamental that the
  • 00:25:29
    fundamental is that the electrons will
  • 00:25:32
    absorb that will go to an higher energy
  • 00:25:35
    so if that goes to an higher energy and
  • 00:25:37
    that higher energy is unfavorable then
  • 00:25:40
    what will happen is that the bond will
  • 00:25:42
    break right but here what happens is
  • 00:25:45
    that in the aromatic amino acid it is in
  • 00:25:48
    the state of C pi interaction okay so
  • 00:25:52
    it's stabilizing electrostatic
  • 00:25:54
    interaction between a cation and the
  • 00:25:57
    polarizable Pi electron cloud of an
  • 00:26:00
    aromatic ring okay so this is in a
  • 00:26:03
    stable Catan Pi interaction and each
  • 00:26:07
    carbon atom will have this P atom over
  • 00:26:10
    orbital overlapping and it is forming a
  • 00:26:14
    conjugated Pi orbital system so this
  • 00:26:17
    creates the delocalized elron cloud so
  • 00:26:20
    since they are delocalized once they
  • 00:26:23
    absorb your uite they go to the higher
  • 00:26:26
    energy level and it helps to make it
  • 00:26:30
    stable means the bonds are stable and
  • 00:26:33
    they do not break down because they are
  • 00:26:37
    delocalized and they can absorb the
  • 00:26:39
    energy and can go to higher energy phase
  • 00:26:43
    and still can would be able to keep the
  • 00:26:46
    bond intact okay so this helps in
  • 00:26:49
    stability after the so delocalized P
  • 00:26:52
    electrons are the ones that are
  • 00:26:54
    responsible so in the why in the so so
  • 00:26:58
    as uh Ria was mentioning that aromatic
  • 00:27:01
    amino acid because of the AR aromaticity
  • 00:27:04
    property but actually not because of the
  • 00:27:07
    aromatic Rings they have a conjugated
  • 00:27:09
    string structures and have a delocalized
  • 00:27:11
    p electrons that whenever after
  • 00:27:15
    absorbtion also they help to after
  • 00:27:18
    gaining energy also that the bond
  • 00:27:21
    remains intact and they can absorb it
  • 00:27:24
    okay so it attracts and uh so it helps
  • 00:27:28
    in the stability and then what we get is
  • 00:27:30
    an enhanced absorption so the tryptophan
  • 00:27:33
    is that what har was mentioning is
  • 00:27:35
    correct and something 279 or around that
  • 00:27:38
    so that is the exact absorption and all
  • 00:27:42
    other uh amino acids do not show this
  • 00:27:45
    structure or do not show this property
  • 00:27:48
    because of the absence of this P
  • 00:27:50
    electrons or the conjugated ring
  • 00:27:52
    structures that's why aromatic amino
  • 00:27:54
    acids are ones which shows the highest
  • 00:27:56
    absorbance at 280 nanometers okay so am
  • 00:28:01
    I clear or anyone has any question so
  • 00:28:05
    here we can see that the Krypt
  • 00:28:07
    absorptions phy absorption and the
  • 00:28:11
    thyrosin absorption which is will we
  • 00:28:14
    remains around 280 whereas philein is in
  • 00:28:18
    the range of around 260 nanometers
  • 00:28:21
    tiptop is around 280 nanometers around
  • 00:28:25
    something exact you can figure it out
  • 00:28:27
    and hosen also in that range so this is
  • 00:28:31
    where our
  • 00:28:33
    particular amino acids gets absorbed the
  • 00:28:36
    absorption of aromatic amino acid okay
  • 00:28:39
    because of this five electrons and the
  • 00:28:42
    delocalized structure that absorption
  • 00:28:44
    also does not let it break away and keep
  • 00:28:48
    it intact okay so any question here
  • 00:28:52
    understood it correctly right so why we
  • 00:28:56
    studied we started with the L flow and
  • 00:28:58
    absorbance is that because we must
  • 00:29:01
    understand what does we mean first of
  • 00:29:03
    all by absorbance second is that we are
  • 00:29:08
    telling and we are stating the fact that
  • 00:29:11
    absorbance is shown by the aromatic
  • 00:29:14
    amino acids at 280 nanometer but we
  • 00:29:17
    should understand the reason behind it
  • 00:29:19
    so why and how the absorption is getting
  • 00:29:23
    increased and 280 nanometer only the
  • 00:29:25
    aromatic amino acids are showing a
  • 00:29:27
    strong absorbance
  • 00:29:28
    whereas other amino acids are not
  • 00:29:30
    showing the absorbance because of this P
  • 00:29:34
    electrons
  • 00:29:38
    okay so is it clear for everyone so if
  • 00:29:40
    you can uh just raise your hand that it
  • 00:29:43
    is clear or uh does anyone of you have
  • 00:29:46
    any doubt no
  • 00:29:51
    right
  • 00:29:53
    great so now what we will do is that we
  • 00:29:56
    are going through the types of of amino
  • 00:29:58
    acids I think it's a very uh common
  • 00:30:02
    question and I think all of you know
  • 00:30:04
    just anyone juster it and then we can
  • 00:30:06
    Skip and go to the next part what is the
  • 00:30:09
    what are the types of amino acids
  • 00:30:10
    according to the diet dietary
  • 00:30:17
    requirements so essential and
  • 00:30:20
    non-essential amino acids
  • 00:30:25
    right essential and non-essential aminy
  • 00:30:27
    right what are essential amino acids so
  • 00:30:31
    essential amino
  • 00:30:33
    acid yes yes Pua go
  • 00:30:43
    ahead correct so Essentials are the ones
  • 00:30:47
    which our body are not able to
  • 00:30:49
    synthesize and are
  • 00:30:51
    requireed by in the diet whereas
  • 00:30:54
    non-essential ones are the ones that can
  • 00:30:56
    be synthesized by our human body from
  • 00:30:59
    other compounds that is mostly other
  • 00:31:01
    precursors and that we do not require to
  • 00:31:04
    intake from our uh diet so like Hine
  • 00:31:07
    isoline Lucine kytopen thionine valine
  • 00:31:11
    iny analine all these are very much
  • 00:31:13
    crucial and that needs to be come
  • 00:31:15
    through our diet so that's why our we
  • 00:31:19
    should have protein in our diets which
  • 00:31:22
    contains these particular amino acids
  • 00:31:25
    that are not able to be synthesized in
  • 00:31:26
    our body for our functioning and
  • 00:31:29
    maintenance of the homeostasis and all
  • 00:31:31
    the tissue cellular functions repair and
  • 00:31:34
    nutrient absorption whereas
  • 00:31:36
    non-essential amino acids are those that
  • 00:31:38
    can be synthesized by the human body
  • 00:31:41
    from other compounds and that's why uh
  • 00:31:44
    it is not absolutely necessary to take
  • 00:31:46
    it but yes of course we can have it okay
  • 00:31:50
    so different metabolic processes enzyme
  • 00:31:52
    production and we know that the amino
  • 00:31:55
    acids as I mentioned already that are
  • 00:31:57
    the sources of the building blocks and
  • 00:31:59
    every repair organs tissues muscles for
  • 00:32:03
    all these things it is
  • 00:32:06
    quite
  • 00:32:09
    important
  • 00:32:11
    right so now yeah sorry
  • 00:32:15
    so yeah so now another concept of
  • 00:32:19
    chirality of amino acids yes so before
  • 00:32:22
    going again so if anyone what is what do
  • 00:32:24
    you mean by kyal
  • 00:32:29
    kyal carbon have you heard about the
  • 00:32:31
    term
  • 00:32:32
    kyal you must have why if
  • 00:32:36
    you when different groups are
  • 00:32:41
    attached is it uh what you
  • 00:32:46
    told the different groups so not
  • 00:32:49
    different groups it should be that the
  • 00:32:52
    four different groups okay so the term
  • 00:32:55
    four is quite important here because if
  • 00:32:58
    you have only H okay so then you can
  • 00:33:03
    change it according anything but it will
  • 00:33:06
    be mirrored
  • 00:33:07
    superimposable so if you have in carbon
  • 00:33:11
    you know everyone of us know that carbon
  • 00:33:13
    has four hands and here if there are
  • 00:33:17
    four different forms of groups that's
  • 00:33:21
    why glycine has no kyal Center if you
  • 00:33:24
    remember right so there must be four
  • 00:33:28
    different groups that will only make the
  • 00:33:31
    carbon atom a kyal one and that will not
  • 00:33:34
    be superimposable with
  • 00:33:37
    the Mage right so now what are so with
  • 00:33:42
    this gets to the configuration of the
  • 00:33:44
    different isomers so first of all uh if
  • 00:33:48
    you just keep on noting down first of
  • 00:33:53
    all that the amino acids that we have
  • 00:33:55
    said that it comes under the vared R
  • 00:33:58
    groups are the ones that leads to the
  • 00:34:01
    change and the different forms then
  • 00:34:03
    comes the different kinds of isomers
  • 00:34:05
    among which due to the carbon and it has
  • 00:34:09
    our four different uh groups attached to
  • 00:34:12
    a single carbon uh atom then it gives us
  • 00:34:16
    a pyal molecule which is if we change
  • 00:34:19
    the orientation of each one of those
  • 00:34:23
    particular molecules then it will be the
  • 00:34:26
    it mirrored image is not super imposible
  • 00:34:28
    to each other so here comes the concept
  • 00:34:32
    of stereoisomers which is the spatial
  • 00:34:34
    Arrangement and iners which are the
  • 00:34:36
    optical isomers and have mirrored images
  • 00:34:39
    that are nons superimposable so anomers
  • 00:34:42
    are both are same they have the same
  • 00:34:46
    molecular formula function physical
  • 00:34:48
    property everything but they mirror
  • 00:34:51
    images are not
  • 00:34:52
    superimposable so what does enomas do it
  • 00:34:56
    enomas rotate the plain polarized light
  • 00:34:59
    in dor rotatory or Lev rotatory met
  • 00:35:02
    methods so L amino acids are
  • 00:35:05
    predominantly found in proteins that is
  • 00:35:08
    which rotates in the Lor rotatory
  • 00:35:11
    methods or the left hand rotation the
  • 00:35:13
    plain polarized right so can anyone of
  • 00:35:15
    you tell where are the mostly D amino
  • 00:35:18
    acids
  • 00:35:20
    found any example of D amino
  • 00:35:26
    acid we are saying that the in the
  • 00:35:29
    proteins
  • 00:35:32
    yes
  • 00:35:35
    he
  • 00:35:38
    ribos no no ribos sugar we are not
  • 00:35:41
    talking about in the amino acid de amino
  • 00:35:45
    acids are prevalent
  • 00:35:49
    where any example you know that D amino
  • 00:35:53
    acids are present
  • 00:35:59
    so so we all know that Al amino acids in
  • 00:36:01
    humans and proteins which we are saying
  • 00:36:03
    that Al amino acids are present so try
  • 00:36:07
    to find out whether uh so you can after
  • 00:36:10
    this class and all you what you can do
  • 00:36:12
    is that you can go ahead and find uh and
  • 00:36:15
    search that whether bacterial proteins
  • 00:36:18
    contain L amino acids or D amino acids
  • 00:36:20
    okay so take you can take this task just
  • 00:36:23
    you can search after your uh this class
  • 00:36:26
    that whether after this live session
  • 00:36:29
    that whether bacteria proteins contains
  • 00:36:32
    L amino acids or D amino acids okay so
  • 00:36:35
    that you
  • 00:36:36
    can uh do it so now what we are going to
  • 00:36:42
    see is that stereo configuration of
  • 00:36:46
    amino acids so one of the amino acids
  • 00:36:49
    and I think that is also very well
  • 00:36:51
    explained in your uh video regarding the
  • 00:36:55
    D amino acids and the L amino acids and
  • 00:36:57
    rotatory and why D rotatory and why
  • 00:37:00
    theas are different but another concept
  • 00:37:04
    is there about the stereo configuration
  • 00:37:07
    that is the absolute configuration that
  • 00:37:09
    refers to the special arrangement of the
  • 00:37:12
    atoms right so here the terms are R and
  • 00:37:17
    S R refers to rectors and S refers to
  • 00:37:21
    Sinister so another which is the
  • 00:37:24
    absolute or the special Arrangement p
  • 00:37:27
    com with the configurations of two
  • 00:37:30
    things one is r and another is s that is
  • 00:37:33
    rectus and Sinister
  • 00:37:37
    right so here how it is determined it is
  • 00:37:40
    determined on the basis of the priority
  • 00:37:43
    rules so what is that priority rule that
  • 00:37:46
    the groups attached to a kyal center are
  • 00:37:49
    ranked according to their atomic number
  • 00:37:52
    okay so they are ranked by their atomic
  • 00:37:55
    number with the highest atomic number is
  • 00:37:58
    assigned the highest priority and the
  • 00:38:01
    lowest atomic number is assigned the
  • 00:38:03
    lowest priority okay so this is the
  • 00:38:06
    configuration to determine the r or s l
  • 00:38:11
    or D is fine what is will be the r and s
  • 00:38:16
    okay so this comes with the priority
  • 00:38:19
    rules that help us in understanding so
  • 00:38:22
    there the highest atomic number is
  • 00:38:24
    assigned by the highest priority lowest
  • 00:38:27
    is assigned by the lowest priority so to
  • 00:38:30
    properly Orient the molecule the group
  • 00:38:32
    with the lowest priority is positioned
  • 00:38:34
    away from the viewer so then we need to
  • 00:38:37
    trace the path from priorities like a b
  • 00:38:41
    c if the path comes clockwise then it is
  • 00:38:44
    R the kyal center is assigned the r
  • 00:38:47
    designation and counterclockwise it is
  • 00:38:49
    receives the S designation okay so what
  • 00:38:53
    priority rules comes into picture is
  • 00:38:55
    that the kyal Center different groups
  • 00:38:58
    that are attached they are marked as a b
  • 00:39:01
    c d on the basis of the highest priority
  • 00:39:04
    which is having the highest atomic
  • 00:39:06
    number and the lowest one with the
  • 00:39:09
    lowest priority and then what it is done
  • 00:39:12
    is that it properly audience the
  • 00:39:14
    molecule the group with the highest is
  • 00:39:16
    first of all taken away and the path is
  • 00:39:20
    traced back and the path if the path is
  • 00:39:23
    clockwise then it is r and if it is not
  • 00:39:25
    then s okay okay so is it clear for each
  • 00:39:30
    one of
  • 00:39:31
    you and
  • 00:39:34
    this have you any doubt regarding it so
  • 00:39:38
    L and D is one but the
  • 00:39:41
    absolute configuration and the absolute
  • 00:39:44
    spatial Arrangement is given by R and S
  • 00:39:47
    okay so dctas and Sinister and this is
  • 00:39:50
    done this is determined on the basis of
  • 00:39:53
    certain priority rules okay
  • 00:39:59
    so now
  • 00:40:01
    can move it forward so after the
  • 00:40:09
    arrangement yeah so after the
  • 00:40:12
    arrangement is done
  • 00:40:14
    okay so after the arrangement and all we
  • 00:40:18
    have seen that D amino acid L amino acid
  • 00:40:21
    special arrangement of amino acids etc
  • 00:40:23
    etc so now comes to the point point of
  • 00:40:27
    the ionization of amino acids right so I
  • 00:40:31
    think all of you have heard must have
  • 00:40:33
    heard about the time term Zer ions so
  • 00:40:37
    now we will look into what is actually
  • 00:40:40
    this Z ions belong to and uh believe me
  • 00:40:45
    that understanding all these basic
  • 00:40:47
    structures will only further help us in
  • 00:40:50
    understanding when we are doing
  • 00:40:52
    understanding the complex concepts of
  • 00:40:54
    understanding the proteins so as you
  • 00:40:56
    mentioned that understanding the
  • 00:40:58
    proteins proteomics for examp
  • 00:41:00
    instance uh relates to the understanding
  • 00:41:03
    of the entire set of proteins in human
  • 00:41:05
    beings and that we can do through
  • 00:41:07
    different structures different
  • 00:41:08
    techniques but each and of this
  • 00:41:11
    technique requires the basic
  • 00:41:13
    understanding of this chemistry because
  • 00:41:15
    then only we would be able to uh break
  • 00:41:17
    down the proteins uh try to analyze
  • 00:41:20
    those proteins try to identify those
  • 00:41:22
    proteins and then only uh able to come
  • 00:41:25
    into some conclusion of identific
  • 00:41:27
    as well as quantification so that's why
  • 00:41:31
    this particular uh thing is quite
  • 00:41:34
    important for us to understand the basic
  • 00:41:36
    chemistry then only we can go ahead and
  • 00:41:39
    study the complex data sets and analyze
  • 00:41:42
    complex samples and complex uh molecules
  • 00:41:45
    okay so here you can see that this is
  • 00:41:49
    the alpha carbon that we all are aware
  • 00:41:52
    about this is R Group Co and the amino
  • 00:41:55
    group so because of this unique property
  • 00:41:58
    of this carboxy group and the amino
  • 00:42:00
    group so this is in always in somewh
  • 00:42:05
    sometimes it is in the positive State
  • 00:42:07
    NSP plus sometimes in negative State Co
  • 00:42:10
    minus sometimes it is in uh positive
  • 00:42:13
    State and deprotonated State and the
  • 00:42:16
    protonated groups right so the basically
  • 00:42:19
    this is measured in terms of pH right so
  • 00:42:24
    this whole concept that this particular
  • 00:42:28
    amino acid will be in protonated form or
  • 00:42:32
    deprotonated form right it will be in
  • 00:42:34
    deprotonated form that is in the acidic
  • 00:42:37
    state or in the protonated form that in
  • 00:42:39
    the basic state is determined by the pH
  • 00:42:43
    so it it is completely dependent on the
  • 00:42:46
    solution it is so the amino acids are
  • 00:42:50
    often referred to as wi ions so contains
  • 00:42:53
    both acidic and bdic groups that allows
  • 00:42:56
    the intramolecular acid base reaction so
  • 00:43:00
    intr molecular not intermolecular so
  • 00:43:04
    please uh pay careful attention to the
  • 00:43:07
    term of intra and Inter when it is inter
  • 00:43:10
    it is between two molecules when it is
  • 00:43:13
    intra means it is within the molecule so
  • 00:43:16
    intra represents anything within so int
  • 00:43:20
    molecular acid based reaction where the
  • 00:43:22
    acidic protone from the carboxilic acid
  • 00:43:25
    protonates the Amine so from the amine
  • 00:43:29
    group gets protonated from the carboxy
  • 00:43:32
    group and the it becomes in the uh
  • 00:43:38
    either it can be in the uh when it
  • 00:43:40
    happens then it is in the neutral State
  • 00:43:43
    or the leric form that you can see in
  • 00:43:45
    the blue when you have the balanced
  • 00:43:48
    charge H+ and minus so this zic property
  • 00:43:53
    is prevalent at physiological pH in
  • 00:43:55
    Aquas media characteristic of living
  • 00:43:58
    organisms and in other polar solvents so
  • 00:44:01
    that is characteristic of living
  • 00:44:03
    organisms and in your other polar sents
  • 00:44:06
    at different pH values amino acids can
  • 00:44:09
    become slightly ionized favoring either
  • 00:44:11
    cic or ionic forms right so different pH
  • 00:44:15
    levels will uh uh different pH levels
  • 00:44:20
    will different will act differently and
  • 00:44:23
    it will favor either cationic forms or
  • 00:44:26
    ionic forms and this PH range at which
  • 00:44:29
    an amino acid is UIC varies depends on
  • 00:44:31
    it specific PKA values so now you have
  • 00:44:35
    understood that it depends on the
  • 00:44:37
    different pH and it forms different
  • 00:44:40
    acidic State and the basic straight and
  • 00:44:43
    it keeps on
  • 00:44:45
    interchanging so can anyone of you tell
  • 00:44:48
    an application on which it is there for
  • 00:44:53
    and an application of this property of
  • 00:44:55
    this uh amino acid to separate different
  • 00:44:59
    proteins or different uh or any kind of
  • 00:45:03
    application if you can uh talk about
  • 00:45:06
    using this property any technique that
  • 00:45:08
    has been developed using this
  • 00:45:14
    property anyone of
  • 00:45:19
    you so how many of you have heard about
  • 00:45:22
    the term Jail uh jail based proteomic or
  • 00:45:26
    SDS ja page jail SDS page how many of
  • 00:45:29
    you have
  • 00:45:32
    heard how many of you have heard the
  • 00:45:34
    term SDS
  • 00:45:37
    page no
  • 00:45:42
    one yeah prya
  • 00:45:44
    yes so what is the principle of SDS
  • 00:45:50
    page PR you can go ahead yeah
  • 00:45:59
    based on their molecular weight right so
  • 00:46:02
    that is one dimensional so how so have
  • 00:46:05
    you heard about 2D or two dimensional
  • 00:46:07
    gel
  • 00:46:14
    electroforesis okay so you are not okay
  • 00:46:18
    so who else have heard about two
  • 00:46:20
    dimensional I think SDS page all of you
  • 00:46:22
    have heard is there anyone who does not
  • 00:46:24
    know SDS page or haven't heard of or
  • 00:46:26
    hearing it for for the first
  • 00:46:27
    time sodium doal sulfate polyamide G
  • 00:46:32
    electris is there anyone who is hearing
  • 00:46:34
    for the first time I would be happy the
  • 00:46:39
    happiest to see if
  • 00:46:42
    to learn that if someone is hearing it
  • 00:46:44
    for the first time then then it will
  • 00:46:47
    give uh give us an opportunity to
  • 00:46:49
    discuss
  • 00:46:50
    and so I am hoping that I am assuming
  • 00:46:54
    that everyone uh knows so so just raise
  • 00:46:58
    your hand and say that how many of you
  • 00:46:59
    have heard about the term 2dl
  • 00:47:02
    electris yes hurry and
  • 00:47:11
    others anyone else have heard about the
  • 00:47:16
    term I could see samika or someone
  • 00:47:19
    raised your hand so you can go ahead
  • 00:47:21
    samic
  • 00:47:22
    sh uh
  • 00:47:31
    just try give a try I have uh given you
  • 00:47:34
    a hint as well that we are uh reading
  • 00:47:38
    about the wiering structure and those of
  • 00:47:41
    which princip which technique has uh
  • 00:47:43
    developed on the basis of this principle
  • 00:47:58
    correct so that will be the amino acid
  • 00:48:00
    will be in which state at that point of
  • 00:48:05
    time correct so the basically it is in
  • 00:48:09
    the range so you know we understand that
  • 00:48:12
    it is a
  • 00:48:13
    pH which
  • 00:48:15
    is the amino acids to be in different
  • 00:48:18
    state so on the basis where that
  • 00:48:21
    particular amino acids particular ionic
  • 00:48:24
    state will be zero that the charge will
  • 00:48:26
    be zero that it will be balanced right
  • 00:48:28
    in the zionic state it will be balanced
  • 00:48:31
    so then there will be no more charge
  • 00:48:33
    separation or the protein won't migrate
  • 00:48:36
    to the other part of the charge
  • 00:48:38
    otherwise what is the case and what is
  • 00:48:42
    the happening is that when the protein
  • 00:48:45
    is positively charged so it will be
  • 00:48:47
    moving towards a negatively charged uh
  • 00:48:51
    particular uh towards the negatively
  • 00:48:54
    charged uh cathod so this this is how
  • 00:48:58
    protein move or the amino acid moves or
  • 00:49:01
    the protein particular that moves but
  • 00:49:04
    when the charge will become zero then
  • 00:49:07
    what will happen is that it will stop
  • 00:49:09
    moving it further and in the two
  • 00:49:11
    dimensional GIS so that is the property
  • 00:49:14
    of the protein but from the concept of
  • 00:49:17
    the amino acid we can understand that
  • 00:49:20
    this uh they are separated on the basis
  • 00:49:22
    of the pH or gradient is formed where
  • 00:49:26
    the proteins are separated to some
  • 00:49:29
    extent where their Pi isric Point
  • 00:49:31
    becomes zero and then further if you
  • 00:49:34
    have a molecular weight based separation
  • 00:49:36
    like the SDS page then they will again
  • 00:49:37
    further separate that we will definitely
  • 00:49:40
    come uh when we are discussing that in
  • 00:49:43
    detail like the gel based protein okay
  • 00:49:46
    so we will have the 2D page 2D d as well
  • 00:49:50
    as the SDS page we will discuss it in
  • 00:49:52
    detail okay but I just give you a hint
  • 00:49:55
    and idea about how it forms so now we
  • 00:49:58
    have talked all about amino acids but
  • 00:50:01
    now we all are in the course of
  • 00:50:08
    proteomics so we are in the course
  • 00:50:12
    ofic we know that we are we are aiming
  • 00:50:15
    that we will be able to understand all
  • 00:50:18
    the proteins in an organism with
  • 00:50:20
    bacteria bead uh virus bead human being
  • 00:50:24
    bead a monkey sh
  • 00:50:27
    dog anyone so we are aiming that we will
  • 00:50:30
    be knowing that all sets of protein
  • 00:50:32
    entire sets of protein present in that
  • 00:50:33
    particular organism for that we have
  • 00:50:37
    understood uh the structure of amino
  • 00:50:39
    acids so now the comes uh so the
  • 00:50:42
    proteins cannot be built without the
  • 00:50:44
    amino acids joining together and joining
  • 00:50:47
    by a very uh bond that is the peptide
  • 00:50:51
    bond right anyone what is the name what
  • 00:50:55
    can be the other name of the peptide
  • 00:50:57
    bond anyone just
  • 00:50:59
    quickly what can be the other name of
  • 00:51:01
    the peptide
  • 00:51:05
    bond the peptide bond can can also be
  • 00:51:08
    called as so what is this reaction
  • 00:51:12
    called and lead to formation of What
  • 00:51:15
    bond what type of bond
  • 00:51:19
    rather so two amino acids are joined by
  • 00:51:22
    what reaction the reaction is known as
  • 00:51:28
    condensation reaction
  • 00:51:29
    right so anyone who does not know
  • 00:51:33
    condensation
  • 00:51:36
    reaction so what this Bond can also be
  • 00:51:39
    termed
  • 00:51:44
    as anyone just give a try what this Bond
  • 00:51:47
    the PTI Bond can also be termed as what
  • 00:51:50
    what type of bond this is what type of
  • 00:51:51
    bond actually
  • 00:51:57
    it is a kind of amide bond
  • 00:52:01
    right so what
  • 00:52:05
    is so peptide bond is nothing but
  • 00:52:08
    composed of amino acids so this is one
  • 00:52:10
    amino acid this is one amino acid link
  • 00:52:12
    by a peptide bond by calent peptide
  • 00:52:16
    bonds and it is sequence are determined
  • 00:52:19
    by TRNA that I think all of you must
  • 00:52:22
    have read or you can read in any
  • 00:52:24
    molecular biology uh books Concepts like
  • 00:52:28
    the TRNA which will come uh will bring
  • 00:52:31
    the amino acids together and the process
  • 00:52:34
    of complete process of
  • 00:52:35
    translation so it is a condensation
  • 00:52:38
    reaction Co group of one amino acid
  • 00:52:42
    reacts with nh2 group of the next and
  • 00:52:45
    what we will do is that it releases H2O
  • 00:52:48
    so here one water molecule is released
  • 00:52:52
    that's why it is the term is
  • 00:52:54
    condensation reaction so bond is formed
  • 00:52:58
    with condensation reaction we co group
  • 00:53:01
    of one reacts with the nh2 group so here
  • 00:53:03
    you can see this is the co part of the
  • 00:53:05
    group this is the nh2 group which reacts
  • 00:53:09
    and releases H2O right so this is the
  • 00:53:12
    condensation
  • 00:53:13
    reaction so inter Terminus is that first
  • 00:53:16
    amino acid rains nh2 group so this is
  • 00:53:20
    the n terminal so here you can see
  • 00:53:22
    please uh pay careful attention because
  • 00:53:25
    this is very very important to
  • 00:53:28
    understand when we will be
  • 00:53:29
    analyzing our data as well in the from
  • 00:53:32
    the complex data sets when we will be
  • 00:53:34
    doing the particular cleavage of certain
  • 00:53:38
    peptides to generate from the proteins
  • 00:53:40
    to generate peptides and then run in
  • 00:53:43
    different modern instruments to get
  • 00:53:46
    understand identify which amino acid it
  • 00:53:48
    is or sequencing of the amino acid and
  • 00:53:51
    quantification of the amino acids this
  • 00:53:53
    concept will be very very useful
  • 00:53:56
    so in terminal is this one which states
  • 00:54:00
    that the first amino acid retains the
  • 00:54:02
    nh2 group and loses the co group to the
  • 00:54:06
    to bond with the second amino acid and
  • 00:54:10
    in this way ultimately when 1 2 3 4
  • 00:54:14
    whatever is being determined to TRNA
  • 00:54:18
    right whatever is being determined to
  • 00:54:21
    TRNA synthesis when it will be all the
  • 00:54:24
    sequence will be covered then the C
  • 00:54:27
    terminal will remain free one place
  • 00:54:29
    where n terminal will remain free n
  • 00:54:32
    terminal will remain free and the other
  • 00:54:34
    place the C Terminus will be remain free
  • 00:54:36
    so that is the last amino acid that is
  • 00:54:39
    known as the C Terminus so a peptide
  • 00:54:42
    bond starts from an N Terminus and ends
  • 00:54:45
    at C Terminus right it starts or begin
  • 00:54:49
    with N Terminus and end at C Terminus so
  • 00:54:53
    the first amino acid retains the nh2
  • 00:54:55
    group and loses group to bond with the
  • 00:54:57
    second amino acid and the last amino
  • 00:55:00
    acid return Co group and prodes nh2
  • 00:55:02
    group with the previous amino acid so it
  • 00:55:06
    has the strong with partial Bond double
  • 00:55:09
    bond character okay so the major thing
  • 00:55:13
    so we which will come in detail now to
  • 00:55:16
    understand the characteristics of
  • 00:55:18
    peptide bond so this is very very
  • 00:55:20
    crucial okay so the characteristic of
  • 00:55:23
    peptide bond to understand is very very
  • 00:55:26
    crucial so it is strong with the partial
  • 00:55:29
    Bond character and it is not broken by
  • 00:55:32
    heating or high salt concentration so
  • 00:55:35
    that we need to understand so this has a
  • 00:55:40
    strong me it is not so we can just by
  • 00:55:44
    heating or something we can uh teat or
  • 00:55:48
    Pro the heating or the peptide bonds so
  • 00:55:51
    it can be broken by strong acids or
  • 00:55:53
    bases at elevated temperatures and
  • 00:55:55
    specific enzymes that is digestive
  • 00:55:57
    enzymes or you Canard I don't know if
  • 00:56:00
    you have heard about the term proteases
  • 00:56:03
    there are different proteases that can
  • 00:56:05
    break this particular Bond so peptide
  • 00:56:09
    bonds are rigid lers stabilizing the
  • 00:56:11
    protein structure and contain partial
  • 00:56:15
    positive charges and partial negative
  • 00:56:17
    charges from the oxygen atoms of carboxy
  • 00:56:20
    groups and hydrogen atoms of amino
  • 00:56:24
    groups so now just a quick question that
  • 00:56:26
    if a peptide bond is formed by a
  • 00:56:30
    condensation reaction that is H2O is
  • 00:56:33
    removed and carboxy group and NH group
  • 00:56:37
    gets joined then with what reaction can
  • 00:56:41
    it Al can it be broken down or the
  • 00:56:43
    peptide bond can be broken down any
  • 00:56:46
    reaction that is coming into your mind
  • 00:56:48
    to denature the peptide bond or break
  • 00:56:51
    down the peptide bond
  • 00:56:55
    yes yes so hydrolysis is one uh reaction
  • 00:57:00
    through which the peptide bonds can be
  • 00:57:02
    denatured that is can be broken down but
  • 00:57:05
    in normal condition it is very very slow
  • 00:57:08
    process and it requires certain kind of
  • 00:57:12
    heating or enzymes mostly what we use
  • 00:57:15
    kinds of uh proteases so one uh task you
  • 00:57:19
    can go ahead and take it Forward before
  • 00:57:22
    going into the complex proteomic when
  • 00:57:24
    you will be doing you will be so I can
  • 00:57:27
    give you a kind of a spoiler that you
  • 00:57:30
    will be hearing the term uh F scene or
  • 00:57:34
    prots okay Li see kotp you will be
  • 00:57:38
    hearing it or if you read any manuscript
  • 00:57:41
    or any read any particular book uh you
  • 00:57:44
    will be coming across this term so one
  • 00:57:47
    uh task you can take it forward so these
  • 00:57:50
    are obviously not related to your
  • 00:57:52
    assignments or those things but
  • 00:57:53
    obviously for your own interest and
  • 00:57:57
    understanding deeper understanding of
  • 00:57:59
    the subject like the trip scene how it
  • 00:58:02
    works at so not at what terminal and
  • 00:58:06
    what after amino acid what how it works
  • 00:58:10
    what I mean to say is that what is the
  • 00:58:12
    exact mechanism of how it works it's
  • 00:58:14
    fine that it works after certain and
  • 00:58:16
    certain amino acids if you just Google
  • 00:58:19
    it you will find that cin Cuts after C
  • 00:58:24
    terminal of this and this amino acid so
  • 00:58:26
    that is not my question or that is not
  • 00:58:28
    what I meant to understand what I want
  • 00:58:31
    you all to find out that what is the
  • 00:58:33
    exact mechanism what is the exact
  • 00:58:35
    reaction it is involved and how it is
  • 00:58:38
    done okay so if you want to go ahead for
  • 00:58:42
    a better understanding you can take this
  • 00:58:44
    question and can try to find out and in
  • 00:58:47
    the subsequent weeks when we will be uh
  • 00:58:50
    meeting and when we'll be discussing you
  • 00:58:52
    can come across and you can uh we can
  • 00:58:55
    discuss okay so that is one task you can
  • 00:58:58
    take it uh forward so now in that
  • 00:59:01
    peptide bond we have seen we have said
  • 00:59:04
    that it is a partial double bond
  • 00:59:06
    character I don't know how many of you
  • 00:59:07
    have given attention paid attention to
  • 00:59:10
    that particular term so it is a partial
  • 00:59:12
    double bond character though it is a
  • 00:59:14
    single uh calent Bond but it is we are
  • 00:59:18
    saying that it is a partial double bond
  • 00:59:20
    character uh it is coming so any can
  • 00:59:23
    anyone of you tell that the particular
  • 00:59:26
    what will be the hybridization state of
  • 00:59:28
    that peptide
  • 00:59:31
    bond does anyone of you like to
  • 00:59:35
    try anyone just give a try all of you
  • 00:59:38
    are aware about hybridization
  • 00:59:46
    right what will be the hybridization
  • 00:59:49
    state of the peptide
  • 00:59:50
    bond according to you according to what
  • 00:59:53
    I
  • 00:59:54
    said uh that is a partial double bond
  • 00:59:57
    character you have you have understood
  • 00:59:59
    right C carboxy group nh2 group yeah har
  • 01:00:04
    I I think you can wait a little bit uh
  • 01:00:08
    because others can also give a try and
  • 01:00:10
    then you can
  • 01:00:11
    tell anyone else I'll come to you Harry
  • 01:00:15
    because but let others also try yes
  • 01:00:23
    Amita SP2 and planner okay okay
  • 01:00:28
    others do you agree if you agree you can
  • 01:00:30
    raise your hand and if you disagree you
  • 01:00:32
    can
  • 01:00:37
    just
  • 01:00:39
    okay
  • 01:00:41
    others so who have no idea you can also
  • 01:00:44
    say that I don't have any
  • 01:00:47
    idea so those who have no idea at all
  • 01:00:50
    that what hybridization State can be
  • 01:00:53
    also can raise your hand
  • 01:00:57
    if you don't raise your hand now then I
  • 01:00:58
    will I have to ask each one by name by
  • 01:01:06
    name okay so soita can why why did you
  • 01:01:11
    told SP2 can you just
  • 01:01:23
    explain you are there
  • 01:01:28
    so can you explain why did you told
  • 01:01:37
    to
  • 01:01:49
    uh correct so I'll explain it
  • 01:01:57
    uh little bit I'm coming to that uh
  • 01:02:00
    question yeah so I will so I have
  • 01:02:03
    already asked you the question of the
  • 01:02:05
    hybridization state so now let us see
  • 01:02:08
    that why uh what is the what could be
  • 01:02:10
    the possible reasons plausible reasons
  • 01:02:12
    for that okay so the characteristics of
  • 01:02:16
    the peptide bonds if we talk about of
  • 01:02:19
    the peptide bomb so first of all it
  • 01:02:21
    absorbs at 192 to 30
  • 01:02:24
    nanometer and subset ility to U be
  • 01:02:27
    radiation okay so as she mentioned it is
  • 01:02:32
    really true that peptide bonds exhibit
  • 01:02:34
    resonance with partial sharing of two
  • 01:02:36
    pairs of electrons between the Amite
  • 01:02:38
    nitrogen and the carboxy oxygen the
  • 01:02:41
    Amite nitrogen and the carboxy oxygen
  • 01:02:44
    there is a partial sharing of the two
  • 01:02:48
    pairs of electrons and this exhibit the
  • 01:02:51
    resonance structure resonating and
  • 01:02:53
    that's lead to the having the partial
  • 01:02:55
    double bond one character so the atoms
  • 01:02:58
    are in the same plane so first of all
  • 01:03:00
    planer that is they are in the same
  • 01:03:02
    plane and hydrogen of the Amite group
  • 01:03:04
    and are trans to each other so again we
  • 01:03:07
    will be now looking further why they are
  • 01:03:10
    trans and why what method they are so it
  • 01:03:14
    was falling and cor determine that
  • 01:03:17
    peptide bonds are rigid and fler so you
  • 01:03:19
    can see that though they have the single
  • 01:03:21
    Bond there could have been the rotation
  • 01:03:24
    but there is a barrier to the rotation
  • 01:03:26
    because of this lone pair of electrons
  • 01:03:28
    being resonating with each other sorry
  • 01:03:31
    and it someh somewhat feels that it is a
  • 01:03:34
    double bond in nature double bond in
  • 01:03:37
    structure so that's why they are not
  • 01:03:39
    able to rotate there is a huge barrier
  • 01:03:42
    to the rotation so this significant
  • 01:03:45
    barrier to rotation as like a double
  • 01:03:48
    bond so then we can said that can you
  • 01:03:51
    get the hybridization State and you have
  • 01:03:53
    said that it is in SP2 hybridization so
  • 01:03:56
    why so as correctly mentioned these are
  • 01:03:58
    resonance hybrids so there is a
  • 01:04:00
    resonating structure so we just have the
  • 01:04:03
    partial double bond characteristics so C
  • 01:04:07
    and N are each SP2 hybridized you can
  • 01:04:10
    see that it is SP2 hybridized and it
  • 01:04:13
    forms a double bond so why it is that so
  • 01:04:17
    SP2 hybridization what is the
  • 01:04:19
    characteristics so they remains planer
  • 01:04:22
    in 120° so you can see the resem L of
  • 01:04:26
    the structure with the structure that
  • 01:04:28
    are General properties of the compounds
  • 01:04:32
    that are in SP2 hybridization right in
  • 01:04:35
    the 120° planner to each other so One S
  • 01:04:39
    orbital and two P orbitals Mak to form
  • 01:04:42
    three equivalent SP2 hybrid orbitals and
  • 01:04:45
    it is known as the trigonal
  • 01:04:47
    hybridization trigonal
  • 01:04:51
    hybridization and these are arranged in
  • 01:04:53
    a trigonal planner geometry
  • 01:04:56
    with 120° angles between them
  • 01:05:00
    right so these are with the
  • 01:05:06
    120° between them and this hybrid
  • 01:05:09
    orbital are 33 % s character and 66.66%
  • 01:05:16
    P character so these molecules with a
  • 01:05:19
    central atom that is linked to three
  • 01:05:22
    atoms and SP2 hybridize exhibit a
  • 01:05:24
    triangular planer shape
  • 01:05:26
    okay so this is the main reason why this
  • 01:05:29
    is particularly SP2 hybridized State and
  • 01:05:33
    this is the structure that is being
  • 01:05:36
    resemblance of the peptide bond okay so
  • 01:05:39
    is there any question or query or any
  • 01:05:42
    thing
  • 01:05:45
    here no right
  • 01:05:50
    okay so then we can move to understand
  • 01:05:54
    that the peptide bond that remains
  • 01:05:57
    mostly in transform right so not in the
  • 01:06:01
    C form so again the peptide bond can be
  • 01:06:03
    present in F or the trans so now why
  • 01:06:07
    they form the have a planner trans
  • 01:06:09
    configuration and with minimal rotation
  • 01:06:12
    so peptide bonds have a planer and in
  • 01:06:15
    the trans configuration which is
  • 01:06:17
    generally having a very minimal rotation
  • 01:06:21
    so NC and Co bonds are the intermediate
  • 01:06:24
    between our single and double bonds that
  • 01:06:27
    is which is having some1 32 nanom Bond
  • 01:06:32
    length and what is happening is that the
  • 01:06:35
    amido
  • 01:06:42
    amido
  • 01:06:44
    yeah
  • 01:06:46
    so
  • 01:06:47
    amidization and bond rigidity prevent
  • 01:06:51
    the free rotation so what is
  • 01:06:54
    totalization
  • 01:06:57
    anyone so we have used this term
  • 01:07:00
    totalization what is the meaning of
  • 01:07:08
    that anyone would like to say what is
  • 01:07:17
    automization Yeah so basically
  • 01:07:19
    the moving of the protons right the age
  • 01:07:25
    from one place to another so this helps
  • 01:07:30
    to these are all preventing the free
  • 01:07:33
    rotation so you can understand that the
  • 01:07:36
    structure of the peptide bond is quite
  • 01:07:40
    very much uh in the format which is
  • 01:07:43
    planer which is rigid and doesn't allow
  • 01:07:46
    for a free uh rotation to go so the
  • 01:07:50
    shared electrons between nitrogen and
  • 01:07:52
    oxygen contribute to the bond uh
  • 01:07:55
    stability so you can see that the
  • 01:07:57
    peptide groups in the planer trans
  • 01:07:59
    configuration so to maximize why they
  • 01:08:02
    are in trans uh state or trans
  • 01:08:06
    configuration because they are to
  • 01:08:09
    maximize the side chain
  • 01:08:11
    distance but the NH group of prolines
  • 01:08:15
    can either CE or trans so only the
  • 01:08:18
    prolin some ring can be either in s or
  • 01:08:21
    trans but maximum peptide bonds are in
  • 01:08:24
    the trans configuration only and these
  • 01:08:27
    transform are in the more common in
  • 01:08:30
    proteins so some Proline residues such
  • 01:08:33
    as permissive can exist in either SS or
  • 01:08:37
    t configuration so this cases you can
  • 01:08:39
    see that some Proline residues are
  • 01:08:42
    permissive to having either of the
  • 01:08:45
    configurations but mostly the pepti
  • 01:08:47
    remain in trans configuration because of
  • 01:08:48
    to maximize the side chain distance
  • 01:08:52
    first of all because the side chain if
  • 01:08:54
    the side chain distance is minimized
  • 01:08:56
    then there will be a stady classes okay
  • 01:08:59
    there will be a hindrance to the stetic
  • 01:09:02
    and there will be the full structure of
  • 01:09:04
    the peptide bond would be uh very much
  • 01:09:07
    uh disoriented and disorganized that's
  • 01:09:10
    why the side chain distance needs to be
  • 01:09:12
    maximized and those peptide bonds are to
  • 01:09:14
    be remain in the trans configuration
  • 01:09:19
    okay so now there's a question of the
  • 01:09:23
    someone asked the question as well and
  • 01:09:25
    this is the experiment of
  • 01:09:27
    anfinsen uh experiment regarding the
  • 01:09:30
    protein folding and how the protein can
  • 01:09:33
    be dened I think this can be answered by
  • 01:09:37
    uh any one of you and then we can look
  • 01:09:39
    at it so before so anyone would like to
  • 01:09:42
    comment on an experiment I think someone
  • 01:09:45
    asked question also so just give a brief
  • 01:09:48
    about uh an sense experiment
  • 01:09:51
    anyone so what were the reents used
  • 01:09:59
    in the beginning only one has asked the
  • 01:10:01
    question I don't remember who was
  • 01:10:04
    uh uh that uh but
  • 01:10:24
    yes p Marto ethanol
  • 01:10:28
    right so what was the role of Ura and
  • 01:10:31
    what was the what is the role of beta
  • 01:10:32
    Marto
  • 01:10:41
    ethanol bet M breaks the disulfide bond
  • 01:10:46
    right okay so what happens when the two
  • 01:10:49
    reagents are given
  • 01:11:11
    correct so it is reduced to the primary
  • 01:11:13
    structure from the folder State and when
  • 01:11:15
    the reagents are withdrawn then it then
  • 01:11:18
    what happens
  • 01:11:39
    correct correct so what we can
  • 01:11:42
    understand is that after the reagents
  • 01:11:44
    are removed what we can say that it is
  • 01:11:48
    its property or stage and which uh which
  • 01:11:52
    is mostly that we can also say that the
  • 01:11:55
    uh the protein folding is quite uh we
  • 01:11:58
    can understand the protein folding in
  • 01:12:00
    invitro state so we will go just uh uh
  • 01:12:05
    see each and every step just by uh
  • 01:12:08
    looking at it we will just brush up so
  • 01:12:10
    this is was done on the protein ribon
  • 01:12:13
    nucleus right so this is the dulfi
  • 01:12:16
    linkages of the tertiary structures
  • 01:12:19
    which we will again come in a while we
  • 01:12:22
    will look at each and each and every
  • 01:12:25
    topic each and every of the secondary
  • 01:12:28
    structure and those structures so here
  • 01:12:30
    the disulfide linkage is there so if we
  • 01:12:32
    have the deducing agent and heating or
  • 01:12:35
    addition of Ura so we will have the
  • 01:12:38
    unfolded ribon nucleus so if we just
  • 01:12:40
    give the reducing agent so the disulfide
  • 01:12:43
    bonds would be breaking so you can see
  • 01:12:45
    that the disulfide bonds which was
  • 01:12:47
    present is getting out and then when
  • 01:12:51
    when we are getting or addition of you
  • 01:12:53
    is unfolding so what is happening is
  • 01:12:56
    that the disulfide bridges in proteins
  • 01:12:59
    are broken by treatment with beta marap
  • 01:13:02
    to ethanol creating new bonds between
  • 01:13:04
    sulfur into mapol molecules so this is
  • 01:13:08
    uh quite a standard procedure I think
  • 01:13:10
    those who are aware about the concept of
  • 01:13:17
    ISP or those they also know the
  • 01:13:21
    principle behind using
  • 01:13:22
    B so this is included in protein
  • 01:13:25
    separation so isds page to ensure the
  • 01:13:28
    dation so aninon what he used is that
  • 01:13:32
    ribon nucleus a to demonstrate that
  • 01:13:34
    protein folding information is contained
  • 01:13:36
    in the amino acid sequence so what he
  • 01:13:39
    wanted to state from this simple
  • 01:13:41
    experiment is that the protein folding
  • 01:13:44
    information is contained in the amino
  • 01:13:46
    acid sequence and this complete
  • 01:13:49
    denaturation require Ura plus two Mar
  • 01:13:52
    ethanol to break dulfi Bridges
  • 01:13:55
    okay so this complete denaturation is
  • 01:13:59
    required to for complete denaturation
  • 01:14:03
    using Ura and two Marto
  • 01:14:08
    ethanol okay so ribon nucleus a refolded
  • 01:14:11
    spontaneously and regain biological
  • 01:14:14
    activity so it was refolded and regained
  • 01:14:18
    the biological activity a removal of Ura
  • 01:14:22
    and two Mar ethanol sh refolding can
  • 01:14:25
    occur in withraw okay so showing that
  • 01:14:29
    refolding can occur in
  • 01:14:34
    withraw so this two so now when if you
  • 01:14:38
    remove just only two Marto ethanol and
  • 01:14:41
    not Ura it resulted in only 1% activity
  • 01:14:46
    recovery due to random dulfi Bridge
  • 01:14:49
    formation right so when you are using
  • 01:14:51
    ribbon nucleus a and the protein folding
  • 01:14:54
    information is contained within the
  • 01:14:56
    primary structure when you are just
  • 01:14:58
    removing the dulfi linkages what it will
  • 01:15:01
    happen is that it will denature the
  • 01:15:05
    dulfi linkages and then if you give udia
  • 01:15:07
    it will completely denature but when you
  • 01:15:11
    uh when you remove udia and uh r that
  • 01:15:15
    markup returnal both it will show
  • 01:15:18
    refolding but when you are removing two
  • 01:15:21
    markup EOL but not Ura it will result in
  • 01:15:23
    only 1% recovery due to the random dulfi
  • 01:15:27
    Bridge formation this suggest that the
  • 01:15:29
    need for correct confirmation to achieve
  • 01:15:31
    full activity so what we could learn
  • 01:15:33
    from this experiments one was that the
  • 01:15:36
    structur conformation in the primary
  • 01:15:38
    amino acid then is that the complete
  • 01:15:40
    removal of this two things and need to
  • 01:15:43
    have a correct confirmation to achieve
  • 01:15:45
    full activity so the enzyme PDI helps
  • 01:15:48
    correct incorrect dulfi bonds allowing
  • 01:15:50
    proteins to unfold and defold correctly
  • 01:15:53
    improving correct protein qu information
  • 01:15:55
    both in vro and in Vivo okay so now we
  • 01:15:59
    are moving into the understanding of the
  • 01:16:02
    structures of protein okay so aninon
  • 01:16:06
    could help us understand that whether
  • 01:16:09
    proteins uh structure information is
  • 01:16:11
    confirmed and the proper structure is
  • 01:16:14
    important to understand and to regain
  • 01:16:17
    biological activity so now if we talk
  • 01:16:20
    about protein structures the protein
  • 01:16:23
    structure as you can see here are in can
  • 01:16:25
    be said into divided into four types
  • 01:16:27
    primary structure secondary structure
  • 01:16:29
    tertiary structure and quary structure
  • 01:16:32
    so now after seeing uh this uh who would
  • 01:16:35
    like to state that what are the uh what
  • 01:16:38
    is the basic differences between each of
  • 01:16:40
    these structure or what are those
  • 01:16:42
    structural forms so in the primary
  • 01:16:43
    structure what is the uh basic structure
  • 01:16:47
    primary structure of amino acids means
  • 01:16:50
    uh what do you mean by primary structure
  • 01:16:53
    of amino acids so you have already seen
  • 01:16:55
    in the
  • 01:16:56
    presentation so what do you mean by
  • 01:16:58
    primary
  • 01:17:00
    structure and in the Anin sense
  • 01:17:02
    experiment also you could understand
  • 01:17:03
    that after protein is denatured you are
  • 01:17:06
    getting the primary a seted yes go
  • 01:17:12
    ahead yes Bas you can go ahead
  • 01:17:26
    yes basti you haveed your hand right you
  • 01:17:28
    can go ahead
  • 01:18:01
    okay right good yeah so you have mostly
  • 01:18:04
    stated uh definition of the structure so
  • 01:18:08
    primary structure is what is just the
  • 01:18:10
    basic sequence or that is the sequence
  • 01:18:13
    that has been what we have already
  • 01:18:16
    discussed that it is from the after the
  • 01:18:18
    translation or the using TRNA we have
  • 01:18:20
    got the sequence so this is contains the
  • 01:18:23
    basic structural information of Amo
  • 01:18:25
    acids within it and followed by the
  • 01:18:27
    secondary structure is
  • 01:18:29
    the holding between the residues of a
  • 01:18:32
    primary structure and then goes to the
  • 01:18:34
    tertiary structure between the different
  • 01:18:37
    regions of that particular polypeptide
  • 01:18:39
    and finally Quon structure between the
  • 01:18:41
    two uh subunits so now what we will do
  • 01:18:44
    is
  • 01:18:45
    that we will go to understand so so
  • 01:18:49
    before going into what is a f and what
  • 01:18:52
    is s uh Bond
  • 01:18:55
    so anyone just quickly you can tell what
  • 01:18:59
    is pi and what is
  • 01:19:00
    s uh angles or side Bonds in the
  • 01:19:05
    proteins in an amino acid primary
  • 01:19:13
    structure so what is a five
  • 01:19:19
    Bond what is five and what is five just
  • 01:19:22
    quickly
  • 01:19:29
    anyone so you all know
  • 01:19:33
    right
  • 01:19:36
    sorry
  • 01:19:45
    H so that is C Alpha that a carbon Alpha
  • 01:19:49
    carbon with the p and Alpha carbon to n
  • 01:19:53
    right so that is the SII and F bonds
  • 01:19:57
    right so this is what let
  • 01:20:00
    ramach or the
  • 01:20:02
    ramachandran uh to decide on the
  • 01:20:04
    structure of the proteins that which
  • 01:20:07
    particular region are we will be able to
  • 01:20:11
    rotate will be able to get and it will
  • 01:20:14
    be the TS and those angles right so the
  • 01:20:18
    n c Alpha and the C Alpha c bonds in a
  • 01:20:23
    polypeptide which are free to rotate
  • 01:20:25
    with the rotations represent by the
  • 01:20:27
    Toran angles pi and side so you just try
  • 01:20:31
    to remember and understand that we have
  • 01:20:33
    said that the peptide bonds that we are
  • 01:20:36
    seeing is quite rigid and have a huge
  • 01:20:39
    amount of barriers to rotation and all
  • 01:20:42
    these things now followed by that what
  • 01:20:44
    we are saying that the NC Alpha so now
  • 01:20:47
    the C Alpha C and the SP and the S
  • 01:20:50
    angles that how they are going to rotate
  • 01:20:53
    in the polypeptide
  • 01:20:55
    that is determined by the ramachandra
  • 01:20:57
    plot so that what uh what how it has
  • 01:21:01
    been determined that it has been
  • 01:21:02
    determined to use computer models to
  • 01:21:05
    verify and S angles systematically to
  • 01:21:08
    identify the St stable confirmations and
  • 01:21:11
    avoiding statically disallowed
  • 01:21:13
    structures where Atomic SP spares how
  • 01:21:16
    that was determined that thetically
  • 01:21:19
    disallowed structures or Atomic spheres
  • 01:21:22
    so the based on vand radi would Collide
  • 01:21:25
    so on the basis of the vender radius
  • 01:21:28
    that where it was going to collide it
  • 01:21:30
    has it was decided and it would be taken
  • 01:21:33
    forward so whichever regions were
  • 01:21:36
    allowed right so what are white areas in
  • 01:21:40
    a ramachandra plot in the white areas of
  • 01:21:43
    the ramachandra plot are that it is
  • 01:21:46
    sterically disallowed confirmations
  • 01:21:48
    where atoms come closer than their V was
  • 01:21:51
    radi except for glycine except for
  • 01:21:53
    glycine the atoms come closer and there
  • 01:21:57
    will be sterically disallowed
  • 01:21:59
    confirmations right sterically disallow
  • 01:22:09
    confirmations so this is so you can see
  • 01:22:11
    in the fourth quadrant there is no place
  • 01:22:14
    where it is allowed region okay so just
  • 01:22:17
    uh see check here so this white space
  • 01:22:19
    whatever white space are there all are
  • 01:22:22
    thetically disallowed because their
  • 01:22:25
    confirmation their atoms cannot come
  • 01:22:27
    closer so only these regions are coming
  • 01:22:30
    closer so red areas are no steric
  • 01:22:33
    classes clashes representing Alpha and
  • 01:22:36
    beta sheet confirmations okay a yellow
  • 01:22:40
    area slightly shorter when radi so this
  • 01:22:43
    is only the red regions that represents
  • 01:22:47
    the no steady classes and Alpha and bet
  • 01:22:50
    sheet confirmations can be there yellow
  • 01:22:52
    areas are what slightly water vanward
  • 01:22:55
    was ready an additional region for the
  • 01:22:57
    left-handed Alpha Helix so this is the
  • 01:23:00
    left-handed for left-handed Alpha Helix
  • 01:23:02
    this is right-handed Alpha Helix region
  • 01:23:05
    allowed regions so Al amino acids
  • 01:23:08
    generally don't form extended left hand
  • 01:23:10
    helices but Glycine asparagine and
  • 01:23:12
    aspartate can adopt this conation due to
  • 01:23:15
    side chain stabilization so Al amino
  • 01:23:18
    acids do not form this kind of
  • 01:23:20
    left-handed extended left-handed Alpha
  • 01:23:22
    elix confirmations but Glycine
  • 01:23:25
    asparagine and aspartate can adapt to
  • 01:23:28
    this confirmation due to the side chain
  • 01:23:31
    stabilization and glycine Laing a side
  • 01:23:33
    chain can cut up F angles in all
  • 01:23:35
    quadrants of the ramachandra plot often
  • 01:23:38
    found in protein turn regions where
  • 01:23:40
    other
  • 01:23:41
    residues would be sterically hindered so
  • 01:23:44
    glycine is only one amino acid that is
  • 01:23:47
    adopt F and S angles in all quadrants of
  • 01:23:50
    the ramachandra plot often found in
  • 01:23:52
    protein turn regions where residues
  • 01:23:55
    would be sterically hindered so if
  • 01:23:58
    question at all comes in any of the
  • 01:24:01
    examinations or anywhere that which
  • 01:24:03
    particular amino acid is only present in
  • 01:24:07
    all the four can be present in all the
  • 01:24:09
    four qu of ramachandran plot then please
  • 01:24:13
    remember that glycine is the only amino
  • 01:24:15
    acid that can be present in each of the
  • 01:24:19
    four quadrants of the rachand plot
  • 01:24:21
    because of its simple nature and it does
  • 01:24:25
    not contain it does not contain any uh
  • 01:24:30
    hindered structure or
  • 01:24:33
    sterically uh kinded regions and it is
  • 01:24:36
    generally found in the protein turns
  • 01:24:39
    where other amino acids will not be
  • 01:24:41
    present because of the St hin okay so
  • 01:24:44
    this is what uh you can try to uh
  • 01:24:49
    understand and uh remember so these are
  • 01:24:53
    the regions which which are the
  • 01:24:54
    disallowed which are the allowed and
  • 01:24:56
    which are extended left hand alysis with
  • 01:24:58
    have St clashes and which does not allow
  • 01:25:02
    for any regions okay so what is the
  • 01:25:05
    secondary uh structure of amino acids so
  • 01:25:10
    secondary structure of amino acids can
  • 01:25:12
    be dbed as refers to regular uh so we
  • 01:25:17
    have understood that the primary is just
  • 01:25:19
    the sequence but a protein uh from an
  • 01:25:23
    experiment also you have understood that
  • 01:25:25
    the to have a biological function a
  • 01:25:27
    protein should regain and reform and
  • 01:25:30
    should have its active structure then
  • 01:25:32
    only the proteins would be able to
  • 01:25:35
    function it biologically and would be
  • 01:25:37
    biologically active otherwise it is not
  • 01:25:40
    possible for the protein with only the
  • 01:25:42
    particular amino acid sequence to have
  • 01:25:45
    its complete function right so now the
  • 01:25:49
    next part comes under the process of
  • 01:25:51
    secondary structure of amino acids and
  • 01:25:53
    again the amino acids or the proteins to
  • 01:25:57
    be in a particular uh angle and
  • 01:25:59
    particular region of the FI angle again
  • 01:26:01
    ramach plot comes into action otherwise
  • 01:26:04
    there will be stetic hindrance and the
  • 01:26:05
    proteins will go in an un favorable
  • 01:26:08
    position and that residue would make the
  • 01:26:10
    protein Disorder so what is uh what are
  • 01:26:14
    the two I think you all are aware about
  • 01:26:18
    about it that the most popular two
  • 01:26:20
    structures of amino acids are alpha
  • 01:26:23
    helics and beta TR are those which are
  • 01:26:26
    very much crucial and which are very
  • 01:26:29
    much uh popular for uh very much
  • 01:26:33
    proteins follow these parts to get it
  • 01:26:37
    forward so for example Alpha Helix which
  • 01:26:40
    is the right-handed uh
  • 01:26:43
    spiral confirmation so backbone NH group
  • 01:26:47
    donates a hydrogen bond to the backbone
  • 01:26:50
    and Co group to the amino acid four
  • 01:26:53
    residues
  • 01:26:54
    earlier so what is that meaning so in
  • 01:26:58
    the primary amino acid sequence you have
  • 01:27:01
    the complete residu so from I to uh n
  • 01:27:05
    from one to n residue so I and the
  • 01:27:08
    hydrogen bond develop between the fourth
  • 01:27:12
    I + fourth residue of that particular
  • 01:27:15
    amino acid that leads to the particular
  • 01:27:19
    Alpha that we will be uh looking at in
  • 01:27:21
    detail whereas beta strand are the
  • 01:27:24
    stretches of polypeptide chains which is
  • 01:27:27
    3 to 10 amino acids long in an almost
  • 01:27:29
    fully extended conformation and adjacent
  • 01:27:33
    beta transform beta sheets that are
  • 01:27:35
    stabilized by hydrogen bonds uh so it
  • 01:27:39
    includes the beta sheet structure in
  • 01:27:40
    your silk proteins which you see that
  • 01:27:42
    the fibroin and the fibrin which happens
  • 01:27:45
    is the from the beta sheet that comes
  • 01:27:48
    into place and stabilization by hydrogen
  • 01:27:51
    bonds connected by turn tight turns and
  • 01:27:55
    Loops so as what I was mentioning so
  • 01:27:59
    this is how the alpha Helix look right
  • 01:28:02
    so if you see this is the one so you can
  • 01:28:05
    follow the number what does it mean the
  • 01:28:08
    alpha heles or what is the meaning of
  • 01:28:11
    the term of alpha heles that what we are
  • 01:28:15
    saying so if we take this particular
  • 01:28:18
    amino acid as 1 2 3 4 5 okay so what I
  • 01:28:25
    have said if you just remember what I
  • 01:28:28
    just now tested is I + 4 the hydrogen
  • 01:28:34
    bond interaction between I and I + 4
  • 01:28:40
    residue is what gives you the alpha
  • 01:28:43
    Helix structure so for that amino acid
  • 01:28:47
    is arranged 1 2 3 4 5 and here is a
  • 01:28:53
    interaction so I one and fifth so you
  • 01:28:56
    can see first and fifth are having one
  • 01:29:00
    hydrogen bond sorry so this is one
  • 01:29:03
    hydrogen bond please uh look uh
  • 01:29:06
    carefully if you have any question or
  • 01:29:08
    any doubt you can ask so one 2 3 4 5 so
  • 01:29:12
    one and five have a bond two and six
  • 01:29:15
    will have a bond so I and I + 4 so when
  • 01:29:18
    it is 2 it is I + 4 = 6 there is a
  • 01:29:23
    hydrogen bond Bond now 3 + 7 there will
  • 01:29:27
    be an hydrogen bond so you can see three
  • 01:29:30
    and 7 finally four and eight then five
  • 01:29:34
    and nine so in this way you can see so
  • 01:29:39
    here is a five and N so in this way the
  • 01:29:41
    structure is formed for Alpha Helix
  • 01:29:44
    whenever Alpha Helix is formed like this
  • 01:29:47
    so what it is there so 1 and fourth 1
  • 01:29:52
    and fifth 2 and six
  • 01:29:54
    three and seven so in this way it keeps
  • 01:29:59
    on going and it is forming the alpha
  • 01:30:01
    Helix if you just go and visualize any
  • 01:30:04
    protein structure you take in pdb or in
  • 01:30:06
    anywhere and if you see this kind of
  • 01:30:08
    alpha Helix you can understand that what
  • 01:30:10
    is the hydrogen bond and interactions
  • 01:30:13
    between which and which residues this is
  • 01:30:16
    after every four residues or I I + 4 so
  • 01:30:20
    if you if you you can remember that it
  • 01:30:23
    is within the inter ction between I
  • 01:30:25
    residue and i+ four residue so if we can
  • 01:30:29
    keep on Counting and this is the
  • 01:30:31
    hydrogen bond and this is how the
  • 01:30:32
    structure is formed so this is the
  • 01:30:35
    right-handed coil for 4 to 40 amino acid
  • 01:30:38
    residues and it is held together by
  • 01:30:40
    hydrogen bonds between Co and NH groups
  • 01:30:43
    of every four after every four residues
  • 01:30:48
    after every four residues and each
  • 01:30:51
    complete turn of the Helix spans 3.6
  • 01:30:55
    residues and it defines the coils
  • 01:30:58
    thickness and turn length defining the
  • 01:31:01
    coils thickness and turn
  • 01:31:10
    length so this stability is dependent on
  • 01:31:15
    correct theic
  • 01:31:17
    configuration so this stability depend
  • 01:31:20
    on on correct static configuration ation
  • 01:31:24
    so the large cryopen thyrosine or SM
  • 01:31:27
    small glycine destabilize the Helix okay
  • 01:31:31
    so this stability of alpha Helix is
  • 01:31:34
    quite very important to be determined by
  • 01:31:38
    the correct static configuration and
  • 01:31:41
    when we have large Copan thyrosine or
  • 01:31:44
    small glycine or groups it destabilize
  • 01:31:46
    the Helix so that's so where we need to
  • 01:31:49
    be that that those amino acids don't
  • 01:31:52
    favor the formation of alpha hel
  • 01:31:54
    Proline destabilizes due to its
  • 01:31:56
    irregular geometry and inability to
  • 01:31:58
    participate in hydrogen bond okay
  • 01:32:00
    because it does not have any uh free end
  • 01:32:04
    okay so that's why so just remember
  • 01:32:07
    which of the amino
  • 01:32:09
    acids uh you don't have to remember you
  • 01:32:12
    have to understand and apply the basic
  • 01:32:15
    concept that in this kind of uh Helix
  • 01:32:18
    the stabilization or the stability is
  • 01:32:21
    quite important and if we have this
  • 01:32:23
    large amino acids are small R groups it
  • 01:32:26
    will definitely destabilize the helix or
  • 01:32:29
    if we have the proline then it will also
  • 01:32:31
    be destabilizing due to its irregular uh
  • 01:32:34
    geometry and inability to participate in
  • 01:32:37
    the hydrogen bonding the
  • 01:32:39
    overall uh typ dipole M of the hel
  • 01:32:42
    caused by individual Co group dipoles
  • 01:32:44
    affect stability stable Alpha heles
  • 01:32:47
    often end with a Charged amino acid to
  • 01:32:49
    neutralize the dipo moment okay so this
  • 01:32:53
    was was all about the alpha eles do you
  • 01:32:55
    have any question or any doubt regarding
  • 01:32:58
    Alpha eles anyone we have clearly
  • 01:33:01
    understood that I and I +4 residue is
  • 01:33:04
    what will Le you to the confirmation and
  • 01:33:08
    it is uh obviously there will be some
  • 01:33:10
    amino acids that will destabilize the
  • 01:33:12
    heling structure like it Proline like it
  • 01:33:15
    glycine because of very small nature and
  • 01:33:17
    then of course we have large like Copan
  • 01:33:20
    and uh like Copan which will dilize the
  • 01:33:23
    hel so now we will be looking into one
  • 01:33:26
    other secondary that the protein
  • 01:33:29
    generally formed at beta sheets so bet
  • 01:33:32
    strands are nearly your linear elements
  • 01:33:35
    of the secondary structure two hydrogen
  • 01:33:38
    bonding so you can see there's
  • 01:33:40
    one linear strand of the polypeptides
  • 01:33:43
    another strand another Strand and they
  • 01:33:45
    are taking the hydrogen bond forming a
  • 01:33:49
    beta sheet can be separated in the
  • 01:33:50
    primary sequence by long segments of
  • 01:33:52
    amino acid and not part of the sheet in
  • 01:33:56
    parallel beta sheets hydrogen bonds are
  • 01:33:58
    slanted in alternate directions and the
  • 01:34:01
    sheet exibits a right-handed twist if
  • 01:34:03
    this contrast with the anti parallel
  • 01:34:05
    shets where H bonds are perpendicular to
  • 01:34:08
    the Strand so we can understand
  • 01:34:11
    the difference between parallel strands
  • 01:34:14
    and anti parallel strands in the
  • 01:34:17
    parallel beta sheet what happens is that
  • 01:34:18
    are slanted in alternate directions so
  • 01:34:21
    you can see slanted in alternate
  • 01:34:23
    Direction and here they are in the anti
  • 01:34:26
    parallel at the perpendicular to the St
  • 01:34:28
    and Mi bet sheet a mixture of both
  • 01:34:30
    parallel and anti parallel hydrogen uh
  • 01:34:33
    bonding so this is what comes across the
  • 01:34:36
    beta sheet so beta sheet will have your
  • 01:34:38
    residues and I will have interconnected
  • 01:34:40
    hydrogen bond that can be either slanted
  • 01:34:43
    or can be perpendicular to each other on
  • 01:34:45
    the basis of the parallel and
  • 01:34:46
    antiparallel strand but in the elix it
  • 01:34:50
    will be within that residue and this
  • 01:34:52
    Loop but in the bet stand there will be
  • 01:34:55
    uh elements and chains of amino acids
  • 01:34:58
    and then finally it will be getting
  • 01:35:01
    matched
  • 01:35:02
    okay so now after that we comes under
  • 01:35:06
    the prary structure of protein so once
  • 01:35:08
    the secondary structure of proteins are
  • 01:35:10
    formed in Alpha Helix and our beta sheet
  • 01:35:15
    so now what we are going to do is that
  • 01:35:18
    we are going to try to understand and
  • 01:35:22
    identify the protein tertiary structure
  • 01:35:26
    so tertiary structure is that is the 3D
  • 01:35:29
    configuration of a protein to
  • 01:35:31
    interaction between residues that may be
  • 01:35:33
    inent so the 3D confirmation comes after
  • 01:35:37
    we get the tary structure of proteins so
  • 01:35:40
    these interactions involve various bonds
  • 01:35:42
    and forces between our groups our groups
  • 01:35:45
    and the backbone the types of bonds and
  • 01:35:49
    interactions so T structures are
  • 01:35:51
    stabilized by hydrogen bonds bander
  • 01:35:54
    walls interactions so in the till in the
  • 01:35:57
    secondary uh thing you can see that the
  • 01:36:00
    bonds that it was formed by the hydrogen
  • 01:36:03
    bonds so the now the bonds that are help
  • 01:36:06
    to regain it or stabilize the structures
  • 01:36:10
    are generally hydrogen bonds hydrophobic
  • 01:36:12
    interactions Vander was interactions
  • 01:36:14
    dulfi Bridges ionic bonds like this
  • 01:36:18
    hydrophobic core formation non-polar
  • 01:36:20
    amino acid cluster at the core of the
  • 01:36:23
    prot to avoid water so this is very
  • 01:36:26
    important so if a question comes like
  • 01:36:29
    this in any concept you can understand
  • 01:36:32
    so just think after uh uh going
  • 01:36:37
    completing this week one that that
  • 01:36:39
    different types of amino acids are being
  • 01:36:42
    made not just to increase the diversity
  • 01:36:45
    or it was not just uh by the nature that
  • 01:36:48
    they had uh nature had tried something
  • 01:36:50
    and have got the different diversity but
  • 01:36:53
    each one of those amino acids of those
  • 01:36:55
    20 amino acids has its own unique role
  • 01:36:59
    the role to make the protein structure
  • 01:37:02
    stabilize some proteins they give extra
  • 01:37:05
    uh uh extra what I can say that rigidity
  • 01:37:09
    or that it does not break like the heat
  • 01:37:11
    shock proteins or those kind of nature
  • 01:37:15
    this 20 amino acids are only on the
  • 01:37:17
    basis of their arrangements are able to
  • 01:37:20
    give them the structural stability to
  • 01:37:23
    form the biological activities to
  • 01:37:25
    perform different biological activities
  • 01:37:26
    so that they remain together they do not
  • 01:37:29
    get break down and they can perform each
  • 01:37:32
    and every activity uh very uh clearly so
  • 01:37:36
    this is where it comes very very
  • 01:37:38
    important the role of each and every
  • 01:37:40
    amino acid and the non-polar amino acids
  • 01:37:43
    these are clustering at the core of the
  • 01:37:46
    protein to avoid water and it is
  • 01:37:48
    stabilized by Vandal forces hydrogen
  • 01:37:50
    bonds ionic interactions between poar
  • 01:37:53
    charged amino acids to contribute the
  • 01:37:55
    overall structure then we have the role
  • 01:37:57
    of primary strcture that we have seen an
  • 01:37:59
    if sense experiment then we have the
  • 01:38:01
    folding intermediates chaperon which
  • 01:38:04
    reaching the stable configuration and
  • 01:38:06
    the folding difference you can
  • 01:38:08
    understand the misfolding can result in
  • 01:38:10
    your various orders like disorders and
  • 01:38:13
    cellular deaths and finally the quary
  • 01:38:16
    structure formation is between the two
  • 01:38:18
    subunits that like the hemoglobins A and
  • 01:38:22
    B subunit it forms a ponary structure
  • 01:38:24
    but still the tary structure is very
  • 01:38:26
    much important and one thing is that the
  • 01:38:30
    protein folding is very much uh sorry so
  • 01:38:35
    the protein s just a minute yeah so the
  • 01:38:37
    proteins uh foldings are very very much
  • 01:38:41
    crucial uh in having the 3D structure
  • 01:38:44
    and they are very much evolutionary
  • 01:38:46
    conserved as well the 3D structure of
  • 01:38:48
    the proteins are pretty much
  • 01:38:50
    evolutionary conserved uh as well that
  • 01:38:53
    helps us in uh getting the data that is
  • 01:38:57
    it help us in uh getting that
  • 01:39:00
    particular structure and the biological
  • 01:39:03
    activity to finally get it captured so
  • 01:39:07
    finally we have the individual uh
  • 01:39:09
    subunit structure we have the individual
  • 01:39:12
    each subunit has its own uh primary
  • 01:39:16
    secondary uh and the tertiary structure
  • 01:39:20
    and then we have the forces that are
  • 01:39:22
    holding the subunits together by
  • 01:39:24
    hydrogen bonds and vs forces specific
  • 01:39:27
    Arrangement and impact of alteration
  • 01:39:29
    okay so you can understand that it is
  • 01:39:31
    quite important to have otherwise it
  • 01:39:34
    will not lead to the proper function and
  • 01:39:36
    proper structure and overall proper
  • 01:39:38
    function of a uh protein okay so the
  • 01:39:41
    forces that are holding subun together
  • 01:39:43
    are quite important individual subun
  • 01:39:45
    structure and those structure
  • 01:39:48
    formation yeah sorry so protein folding
  • 01:39:52
    if I talked about in just a brief so
  • 01:39:55
    this is a process linear polypeptide
  • 01:39:58
    transforms into functional
  • 01:39:59
    threedimensional structure I think all
  • 01:40:01
    of you are aware of it so protein
  • 01:40:03
    folding is basically nothing but the
  • 01:40:04
    linear polypeptide chain that we get
  • 01:40:08
    it's to be converted into a linear
  • 01:40:10
    polyte chain and is transformed into a
  • 01:40:13
    functional threedimensional
  • 01:40:14
    structure and initial and final States
  • 01:40:17
    will be that the proteins initially
  • 01:40:18
    exist as unfolded polypeptides or random
  • 01:40:21
    foils after translation and they acquire
  • 01:40:23
    a stable three dimensional structure
  • 01:40:25
    known as the native
  • 01:40:27
    state uh then we have the information
  • 01:40:29
    contained in the primary structure role
  • 01:40:31
    of capons and evolutionary conservation
  • 01:40:35
    as I mentioned and the importance of
  • 01:40:38
    correct folding and the ionic
  • 01:40:39
    interaction and the dulfi bridges okay
  • 01:40:43
    so this we will find in quite uh uh in
  • 01:40:47
    the reducing so you can see that in the
  • 01:40:49
    reducing environment you won't find it
  • 01:40:51
    but where you need to hide provide High
  • 01:40:54
    stability and all there we will be
  • 01:40:55
    finding so now there is another concept
  • 01:40:58
    of lethal's paradox and energy uh
  • 01:41:02
    Landscapes so will anyone of you would
  • 01:41:04
    like to just give a brief idea of leen's
  • 01:41:09
    paradox you have gone through this in
  • 01:41:11
    the video
  • 01:41:13
    right have you gone through this in this
  • 01:41:16
    uh in the video
  • 01:41:28
    huh so what is 11's
  • 01:41:32
    Paradox or the energy Landscapes related
  • 01:41:35
    to protein
  • 01:41:39
    folding just
  • 01:41:43
    try so any reaction to happen should be
  • 01:41:47
    thermodynamically stable or favorable
  • 01:41:49
    right do you agree with my statement or
  • 01:41:52
    not
  • 01:41:55
    is there anyone who does not agree to my
  • 01:41:59
    statement that any reaction to happen it
  • 01:42:01
    should be thermodynamically
  • 01:42:07
    favorable agree
  • 01:42:11
    right so what we are try in the living
  • 01:42:15
    Paradox and the enery Landscapes is that
  • 01:42:17
    this thought experiment highlights your
  • 01:42:20
    problem of finding your stable energy
  • 01:42:23
    configuration for proteins where an
  • 01:42:26
    exhaustive search to all possible
  • 01:42:28
    conformations would be imprac time
  • 01:42:31
    consuming so what is that if we try to
  • 01:42:34
    find out the uh finding the stable
  • 01:42:38
    energy configuration for our proteins so
  • 01:42:41
    exhaustive search through all possible
  • 01:42:43
    confirmations would be very much
  • 01:42:45
    impractically time consuming so what it
  • 01:42:49
    is there the protein folding efficiency
  • 01:42:53
    despite the vast number of potential
  • 01:42:58
    confirmations proteins fold quickly into
  • 01:43:01
    their native States even in complex
  • 01:43:05
    structures so despite the vast number of
  • 01:43:08
    potential
  • 01:43:10
    conations proteins fold quickly into
  • 01:43:12
    their native States even in their
  • 01:43:14
    complex structures so the rapid folding
  • 01:43:18
    process suggest that protein transitions
  • 01:43:20
    are guided toward stable States through
  • 01:43:22
    an EV energy landscape rather than
  • 01:43:25
    through random search okay so they are
  • 01:43:29
    rapid folding process should be that the
  • 01:43:32
    transitions are guided towards F
  • 01:43:34
    State through an uneven landscape and
  • 01:43:38
    rather than through random s okay so
  • 01:43:40
    this is basically to understand that the
  • 01:43:42
    if you try to find out the possible
  • 01:43:44
    States so it should be guided that which
  • 01:43:47
    will be the favorable and should not be
  • 01:43:50
    too much random otherwise it will be a
  • 01:43:52
    paradox that it will
  • 01:43:53
    not possible uh to find a stable energy
  • 01:43:57
    configuration so for each configuration
  • 01:43:59
    we compute so QR and R then average and
  • 01:44:04
    repeated for zero and Which is less than
  • 01:44:06
    the one
  • 01:44:08
    okay so molecular chaperons are those
  • 01:44:11
    which are conserved proteins that assist
  • 01:44:13
    in the folding so these are plays a very
  • 01:44:17
    huge uh role when there is for the
  • 01:44:20
    assist in the folding of the newly synth
  • 01:44:23
    proteins and preventing misfolding under
  • 01:44:26
    normal conditions and stress such as
  • 01:44:28
    high temperatures so any change in the
  • 01:44:31
    chaperons would be also very much
  • 01:44:33
    crucial and can be taken then assistance
  • 01:44:36
    during stress that the chaperons help
  • 01:44:38
    maintain protein stability and proper
  • 01:44:40
    folding even when cells are exposed to
  • 01:44:42
    sful conditions and significant advances
  • 01:44:46
    have been made in understanding the ATP
  • 01:44:48
    dependent mechanism used by hsp70 and
  • 01:44:51
    chaperon families of chaperons
  • 01:44:58
    and then Cooperative folding hsp70 and
  • 01:45:00
    chonis can work together to facilitate
  • 01:45:02
    the correct folding of new polypeptide
  • 01:45:07
    CH
  • 01:45:09
    okay so as I mentioned so I'd like to
  • 01:45:13
    end uh towards uh this uh today's uh
  • 01:45:16
    thing so there is the omix technology so
  • 01:45:19
    as we have started with I would like to
  • 01:45:23
    uh finish it there only so we have
  • 01:45:26
    understood the basic principles of
  • 01:45:28
    chemistry protein chemistry amino acids
  • 01:45:31
    and all where we are going to take it
  • 01:45:33
    forward for understanding towards the
  • 01:45:36
    entire set of the proteins present in an
  • 01:45:39
    individual so there are different omix
  • 01:45:42
    Technologies so just if I give you a
  • 01:45:44
    brief that it is not uh today or that
  • 01:45:47
    certainly we have come across this idea
  • 01:45:50
    that if we can understand the entire set
  • 01:45:52
    of the proteins we can do something very
  • 01:45:55
    groundbreaking and we can come across to
  • 01:45:58
    certain extent so it all started when
  • 01:46:01
    people when scientists thought that if
  • 01:46:05
    we understand the genetic sequence or
  • 01:46:07
    the DNA sequence of an individuals then
  • 01:46:10
    our entire lot of problem can be solved
  • 01:46:14
    and we can easily come and to can
  • 01:46:18
    understand and can tackle many diseases
  • 01:46:20
    so it started all in '90s and in 2000s
  • 01:46:24
    we could complete the Human Genome
  • 01:46:26
    Project but it was a kind of shock for
  • 01:46:29
    the scientist because it was found out
  • 01:46:31
    that the sequences are quite similar in
  • 01:46:34
    nature the genomic DNA sequences are
  • 01:46:37
    quite similar and there are not much
  • 01:46:39
    changes between the individuals so then
  • 01:46:42
    came the picture of other om
  • 01:46:44
    Technologies specifically the field of
  • 01:46:46
    omic proteomic which stated that
  • 01:46:50
    the after the gene or the DNA sequence
  • 01:46:53
    it is the proteins that are the plays
  • 01:46:56
    the roles of particular functional and
  • 01:46:59
    the structural role in an individual so
  • 01:47:02
    this understanding of this is will be
  • 01:47:04
    quite much useful then comes the
  • 01:47:06
    transcriptomic where the gene expression
  • 01:47:09
    that is quite directly or indirectly
  • 01:47:12
    linked with the protein expression and
  • 01:47:14
    the uh proteins and then finally now the
  • 01:47:18
    emerging field of metabolomic where the
  • 01:47:21
    metabolites or the function level of The
  • 01:47:23
    small molecules are also come into
  • 01:47:27
    playing into pictur that which also uh
  • 01:47:31
    is going you to uh understand uh the
  • 01:47:34
    phenotypic effect at an uh at a very uh
  • 01:47:38
    later level at a very uh level you can
  • 01:47:41
    understand the metabolic disorders that
  • 01:47:42
    are being in place uh completely M
  • 01:47:46
    today's date uh so we all can understand
  • 01:47:49
    at each layer it and whatever layer we
  • 01:47:52
    add
  • 01:47:53
    we keep on adding the complexity genome
  • 01:47:56
    epome transcript prot metabol But
  • 01:47:59
    ultimately this gives us a picture of
  • 01:48:02
    all the uh curated things and in a
  • 01:48:05
    Precision format and uh very much
  • 01:48:09
    important uh required so these are the
  • 01:48:12
    omix Technologies I think you will be
  • 01:48:14
    going to the omix based Technologies
  • 01:48:17
    among the proteomic so you have this
  • 01:48:19
    course we will be learning introduction
  • 01:48:23
    to proteomic in quite detail uh so you
  • 01:48:26
    can understand the proteins its role its
  • 01:48:29
    place and its functions and then
  • 01:48:31
    definitely uh you can explore other
  • 01:48:34
    techniques as well as well in this
  • 01:48:37
    semester only I think there there is
  • 01:48:39
    another more course ongoing that is the
  • 01:48:41
    proteogenomics which com which combines
  • 01:48:44
    the two technologies proteomics and
  • 01:48:47
    genomics to now much comprehensive
  • 01:48:50
    information yeah so if you have any
  • 01:48:52
    question related to this week's doubt or
  • 01:48:54
    today's uh this live session or
  • 01:48:57
    anything uh you are free to do so uh so
  • 01:49:02
    please uh let me know that if you have
  • 01:49:04
    any doubt any
  • 01:49:11
    questions no
  • 01:49:14
    right everything is uh
  • 01:49:21
    clear okay so then I think uh we
  • 01:49:32
    can yeah so I think we can uh
  • 01:49:39
    then uh end today's class and I think we
  • 01:49:42
    can meet again in the next week so
  • 01:49:45
    hopefully uh as I have mentioned that
  • 01:49:47
    you can go ahead and ask uh different uh
  • 01:49:51
    search like specifically the question
  • 01:49:55
    that I said like the trip scene how it
  • 01:49:56
    works how it what reaction it breaks
  • 01:49:59
    down okay because this all will be uh
  • 01:50:02
    coming in the consequent weeks and we
  • 01:50:05
    can look into it okay so I think then we
  • 01:50:08
    can
  • 01:50:10
    end today's class and if you have any
Tags
  • protéomique
  • acides aminés
  • structures protéiques
  • misfolding des protéines
  • loi de Beer-Lambert
  • chaperons moléculaires
  • paradoxe de Levinthal
  • interactions protéiques
  • techniques analytiques
  • concepts de base