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.

Week 1 Proteomics Live Session

01:50:13

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

Ringkasan

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.

Takeaways

📅 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.

Garis waktu

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.

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Peta Pikiran

Pertanyaan yang Sering Diajukan

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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Teks

Gulir Otomatis:

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
00:06:20
evolved and how it is still rapidly
00:06:22
evolving and progressing for
00:06:25
understanding of the proteins at
00:06:27
different level at different states uh
00:06:29
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