Proteins


Hi. It’s Mr. Andersen and in
this video I’m going to talk about proteins. Proteins are incredibly important because
that’s what we’re made up of. When you look at me you’re looking at my proteins. We just
completed the human genome project and we figured out the DNA in a typical human but
now we’re headed into what’s called the proteom project where we try to figure out what these
proteins made up of and what do they look like three dimensionally. This used to be
an incredibly hard process. This is John Kendrew here putting together a model for myoglobin
and he had to do it by hand. We now do a lot of this with computers. But you can help.
At the end of this video I’m going to show you a program called Foldit and you can actually
build and fold proteins that are going to be used in scientific research. And so it’s
a really cool thing. And it’s a really cool time in reference to proteins. But let’s start
by building a little bit of knowledge. Proteins are made of amino acids. And most seventh
graders understand this. They’re the building blocks of proteins. But where do we get those
amino acids? We get them in our diet. And so basically we eat proteins. We break them
down into amino acids and then we can weave those back together again into the proteins
that make us. And so when you’re looking at me, the amino acids in my skin, used to be
part of my food. And so I literally am what I eat. Now here’s five different amino acids.
There are a total of twenty that we use in life, but here’s five basic amino acids. When
I show this to my students they tend to get a little bit overwhelmed because it’s too
much chemistry here on one page. But let’s try to figure out the things that are the
same on this page. And so basically if we were to look at the middle of each of these
we find that there’s a carbon with a hydrogen attached to it. We call this carbon alpha
carbon. It’s going to sit right in the middle. What else is the same in every amino acid?
Well on the left side we have a nitrogen attached to two hydrogens. We call this an amino group.
And then if we look on the right side we have what’s called a carboxyl group. And so basically
every amino acid is going to have these three similar parts. And so the only thing that’s
going to be different is going to be what comes off the bottom. And we call that the
R group. And so all amino acids are the same except what comes off here. And that gives
it different properties. And so let’s kind of see how they’re put together. And so when
I build proteins inside my body, I’m doing that with amino acids. And we use something
called dehydration synthesis to do that. And so let me move this one over here. Basically
what we do is we position one amino acid right next to an amino acid. You can see here that
there is two hydrogens and an oxygen here and you know that in chemistry if we have
two hydrogens, H2O that’s simply a water. And so what we can do is we can lose that
water. Now it’s not as simple as that. This whole thing sits inside a ribosome. So there’s
a giant enzyme around the outside of it. But let’s attach another one. So now we bring
another one right next to it. You can see that the hydroxyl group or the carboxyl group
is attaching to the hydrogen. We’re going to lose a water and then we’re going to form
another covalent bond. And then we put another one next to it. We lose another water, we
form a covalent bond and we do that again and now we have what’s called a polypeptide.
And so each of these individually are called a peptide. But if we attach them all together
we have a polypeptide. And you can see that the strand across the top looks the same.
It looks uniform, but the only thing that’s going to be different in each of these is
going to be the R group, the trails off the bottom. So where does this occur? Well basically
these are the amino acids. This would be the ribosome in a cell and all life does this.
Basically you have these little tRNAs that will bring their amino acids in and then we
attach them together. And when you have a bunch of amino acids attached together, you
have a polypeptide. And that polypeptide will eventually fold into a protein. And so here’s
our five amino acid sequence right here. These are each going to have different chemical
properties. And so for example, this one right here, threonine is going to be polar. What
that means is it’s going to have a charge. If we look at alanine right down the way this
is going to be nonpolar. And so why is that important? Well if you’re polar then you’re
hydrophilic. That means that water is going to be attracted to you. In other words we’re
going to find threonine in the presence of water. But alanine, since it’s got this methyl
group right here, it’s not going to be attracted to the water and so it’s going to hide from
the water. Or if we look at the aspartic acid, it’s going to have a negative charge. And
if we look at the lysine over here it’s going to have a positive charge. And so these two
things or these two amino acids are found in the same polypeptide and they’re going
to try to get next to each other because the positive and the negative are going to attract.
And so what you end up getting is a three dimensional protein. The middle part, so this
brownish tan part in the middle is going to be the back bone. And that’s going to be again
made up of all of the parts of the amino acid that are the same so the amino, the alpha
and the carboxyl group over and over and over again, but all of these things on the outside
that are trailing off are going to be the R groups. These are going to be these residue
groups that kind of fold off the end. And so this right here would be a polypeptide.
This would be a number of different amino acids attached together and these usually
have thousands of amino acids in a typical protein like hemoglobin would be an example
of one that’s found in your blood. And so basically this will fold into a three dimensional
shape. And what I tell students is a polypeptide is just going to be this sequence of those
amino acids and once it’s folded into a specific shape then we can call it a protein. And so
the first, maybe you have read it, there are four levels of structure in a protein. And
so let me talk you through that first and then I’ve got a little model that will hopefully
help. And so the primary structure is going to be the order that those amino acids are
bonded together. The next thing we have are what are called alpha helixes and beta pleated
sheets. And we call that the secondary structure. And so a helix looks like this. A beta pleated
sheet is going to be two sides that are attached to each other and these little dots in the
middle are going to be hydrogen bonding between adjacent sides of that polypeptide. And so
this is the structure that comes out first. It’s going to be linear. Next we have the
alpha helixes or the beta pleated sheets. And then we have the tertiary structure. The
tertiary are the third level of structure, is going to be all of those R groups interacting
and so maybe we have one that’s hydrophobic. It’ll hide to the middle or hydrophilic on
the outside. We’ll have disulfide bonds. We’ll have positive attracting to negative. This
is the third level of structure. And then finally we have quaternary structure. Maybe
we have this one polypeptide together or this protein together with another protein. So
hemoglobin’s an example of that made of a number of different subunits. And so here’s
my little model. And so if you look at this model you can think of this being a polypeptide.
So it’s made up of amino acid after amino acid and then it’s going to have all the R
groups on the underside. Those are going to be the only things that are different, all
these R groups coming off the bottom. And so basically, primary structure like this.
Secondary structure is going to be the alpha helixes and the beta pleated sheets. And so
an alpha helix will look like this. What’s holding that in place is simply going to be
the hydrogen bonds. And then we’re going to have a beta pleated sheet. A beta pleated
sheet might look like something like that. So there’s going to be hydrogen bonds between
here and here. But maybe this right here is a real hydrophobic R group, and it’s going
to fold right to the middle and then this might be hydrophilic. It’s going to fold to
the outside. We might have positive attracted to negative then we eventually have a three
dimensional shape of a protein. Now this may combine with other proteins. But what’s cool
about proteins is their structure fits their function. If it doesn’t have this structure,
if we heat it up, if we cool it, if we change the acidity, basically it will fold apart.
We call that denature and then it doesn’t work anymore. And so I said at the end you
could help in science. So there’s a program called Foldit. I’m going to launch it and
I’ll be back in just a second. And so in this program what you’re given is a simple polypeptide.
So we have two amino acids and then this is going to be the R group. And what you do in
this video game is you try to make the R groups happy. So I’ve already cleared level one.
So let’s go on to level 2. You can download this for Mac, Lynx and Windows. Let me quickly
turn this one around. You can see here that we have a couple of, let me get the help out
of the way, you have a couple of different amino acids and then their R groups. I can
pull those apart and they’re going to be a little bit happier and then I can clear the
level. And so what are you really doing. As I play this game I can talk, basically what
you’re doing is you’re learning the rules of protein folding, but these problems are
going to get harder and harder and harder. You can see an alpha helix here. And so what
you can do is you can get really good at folding these proteins. And what’s neat about this
is people are playing Foldit hour and hour after hour. And it hit the news last year
where a couple of protein folders, probably a team of protein folders decoded the shape
of a really important enzyme in HIV infection. And so it’s plausible that in the future gamers
are going to win a Nobel prize for the work they do on protein folding. Because we know
the primary structure of proteins, but we don’t have any idea of how the three dimensional
shape is put together. And computers are good at this but it turns out that humans are maybe
a little bit better. And so those are proteins and I hope that was helpful.

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100 thoughts on “Proteins

  1. I don't know why I nearly cried when he started explaining the structures. Watching this video made me feel so enlightened I actually finally understand proteins! You, sir, are a pure scientist and insanely good teacher. Thank you so much.

  2. This was an absolutely incredibly well done and well explained video. Being in AP Bio, the class moves so fast and we don't have a lot of time to review key concepts like this so a lot of things go over my head. So, thank you so much. You didn't stutter once or mix up names and it was just genuinely very well done!

  3. [email protected] Alexander Kushelev Online service PROTEIN PICOTECHNOLOGY http://nanoworld.org.ru/topic/1699/
    The Picotech program can not completely replace X-ray structural analysis. However, it greatly strengthens the weakest points of the X-ray diffraction, namely, it shows reliably the secondary structure and the short-range order of the arrangement of the atoms of the tertiary structure at the time of assembly of the protein molecule by the ribosome.
    The sensitivity of X-ray structural analysis is such that it does not notice not only individual atoms, but also individual amino acid residues. Moreover, the "tails" of protein molecules that do not crystallize, the PCA generally "does not see", and these "tails" can consist of up to 50 amino acid residues.
    A special class is formed by 97% of protein molecules that do not crystallize. About them, the PCA simply does not know anything, and the Picotech program also reliably shows their secondary structure and short-range order of the arrangement of atoms in the tertiary structure.
    Your application must contain only the code of the protein of interest to you from the PDB database, or mRNA for it
    We will model your protein complex with ligands of any nature
    The lead time for the order is 1-7 days, depending on the complexity of the project.
    Digest https://picosoft.nethouse.ru/

  4. So if proteins have different hydrophobic/hydrophilic parts… does this ultimately determine whether or not it may pass through a selectively permeable membrane? Or do proteins not leave the cell at all?

  5. There is a tiny thing that I don't understand, why the shape of the protein does determine it's function even though it has the same chemical structure "same AAs" ??

  6. i almost cried during the video. THANK YOU MUCH!!!! THANK YOU SO MUCH FOR THIS VIDEO, THIS VIDEO BRIGHTENS UP MY FUTURE!!! GOD BLESS YOU PAUL!

  7. Excellent lecture except for the use of the word 'cool' twice. Very very unscientific vernacular. Used 'neat' once which is fine. Drop the use of the word 'cool' from your lectures please. 95 % of the people whom I have heard use the word cool have been dumb dumb's. You, of course, being in the 5% who are not. Could you imagine a heart surgeon saying 'cool' several times while performing open heart surgery on a loved one.
    Use of that word is for dope smoking kids….'coooooool man……coooool'. Thanks. Again, great lecture.

  8. Thank you for doing these videos! You’re not just a chemist. You are a good teacher! Very clear explanations. I wish all campuses just had Mr. Anderson’s videos for their lectures on chemistry.

  9. Wake Up & Smell The Amino Acids

    One way to classify “special” smells is to smell the twenty

    basic twenty amino acids, remember them, and classify any

    “special” smell under the category of one of the twenty amino acids.

    I did that over forty years ago, and I have tables of correspondence

    tables that have the twenty basic amino acids corresponding

    to analogous things:

    > 1. itza, don, decider, alanine, dice: 4&2

    > 2. imix, drun, distributor, glycine, 6&1
    > 3. ik, ceph, memory, aspartic acid, 3&3
    > 4. akbal, graph, encoder, tryptophan, 3&5
    > 5. kun, un, extruder, hydroxyproline, 1&1
    > 6. chachuen, fam, EPR, methionine, 6&5
    > 7. cimi, orth, supporter, tyrosine, 6&2
    > 8.*oc, tal, producer, threonine, 4&4
    > 9. lamat, vau, internal trn., valine, 5&5
    > 10. muluc, gon, output trn., glutamine, 4&5
    > 11.*manic, pe, ingestor, lycine, 4&6
    > 12. chuen, ged, storage, phenylalanine, 2&5
    > 13. eb, med, channel&net, asparagine, 3&6
    > 14. ben, gizga, EPA, cysteine, 1&3
    > 15. ix, ur, reproducer, proline, 2&3
    > 16. menn, mals, decoder, serine, 6&6
    > 17. kib, veh, motor, histidine, 1&2
    > 18. caban, pal, boundary, glutamic acid,1&5
    > 19. eznab, nahath, input trn., leucine, 2&2
    > 20. cuac, ger, associator, isoleucine, 4&1
    > 21. ahau, gal, converter, arginine, 4&3
    > *: These have been exchanged in modern times. EPR is
    > Entropy Prodction Rate. EPA is Entropy Production
    > Acceleration. And, trn. is transducer.

    These words have meanings in different languages. For example, let’s take the last one here,

    #21, ahau means flower, and is one of the twenty Mayan calendrical symbols.
    It was amazing; Dr. John Dee, in the Sixteenth Century, presented the Enochian alphabet,

    whose names don’t sound like the letters they represent, but, the names of these twenty-one

    letters mean the same as Dr. James Miller’s subsystems in his book

    “Living Systems”, the primary text book of living systems dynmaics.
    For example in #21 the word “gal” is the pre-Aryan word for the living systems subsystem the

    “converter”. One of the twenty amino acids produced from the DNA code, in this case “arginine”,

    is represented here. The extra amino acid in this system is hydroxyproline,

    which is produced from a code in the “junk” DNA, the most

    important product of the “junk” DNA.
    The DNA code is composed of combinations of four nucleic acids, giving 64 different

    combinations, like the Yi Jing. But, most of the basic 20 amino acids are produced from more

    than one of these combinations. These 20 amino acids compose proteins which build the body and

    assemble other compounds together to compose our complete body.
    There are seven levels of living systems: cells, organs, entities (like us, animals, and plants),

    groups (like families, gangs, teams, etc.), organizations, societies, and suprasocietal living

    systems. All of these depend upon their 21 subsystems. If any subsystem is missing, a higher living

    system must provide a substitute, or, that living system with the missing subsystem will die.
    The number combinations at the end of each line of correspondences represent the combinations

    of dice symbols, which have symbols to represent them: 1, . ; 2, U ; 3, / ; 4, O ; 5, X ; and 6, = .

    You will notice that these symbols span the usual dice symbols.
    Now we combine these six into 21 symbols. The way I’ve seen the 4&3 drawn is a circle with a

    vertical diameter, which also represents the lette D. So, each one of these also represents a

    letter. Also, of coincidence for English speaking people, the compination for B is 4&6, which

    is a cicle with a horizontal parallel in it that makes this symbol look like a bumble bee (B).
    Since we use these subsystems all the time it is organizing to notice them. For example, when

    we go grocery shopping for our family, we become the ingestor by getting the groceries, extruder

    by extruding the money to pay for the groceries, distributor by bringing the groceries to our

    family, and then we use the storage subsystem of our family (group) by storing the groceries

    where they are stored. And, if we decided what to buy, we were

    also the decider for our family.
    But, every group, organization, society, and suprasocietal living system, has a decider that has

    been called a group mind. The Greek for “group spirit” is “demon”, which comes from the Greek

    root “dem” from which we get the word “democracy”. So, we have the group mind to

    help us. Then, that’s literally “demonic”.
    The group entity is a magnetic flux circulating through all the medullas in the brains of all

    the group’s members. But, us Christians are only supposed to have Jesus Christ as our group mind,

    “having the mind of Christ”, and, being members of the “Body of Christ”.
    In the Middle Ages the ranks of these fallen “angels” were defined. The demon of a group was

    called an angel; for an organization, an archangel; for a society, a principality;

    and for a suprasocietal living system, a power.
    Now you can see what was meant, “We fight not flesh and blood; we fight principalities and powers”.

    Smelling licorice is like, but easier than, transcendental meditation. Licorice is synesthetically

    onomatopoeic to a hollow cylinder, and it stirs closed circuitry in the brain that

    goes confluent with the circuit that is the entity so that near nonexistence, nirvana,

    is experienced. Everything is actually striving for nonexistence.

    Nonexistence is the ultimate essence of pleasure. The corresponding sound, the sound of a hollow

    cylinder, pronounced “eyennn”, like the German word for one, “ein”, means “nothingness”,

    “aleph yod nun”, in Hebrew, and is onomatopoeic by meaning a well, but, it also means an eye and a ring.

    The movie “The Ring” plays upon this, the “lost word”.

  10. Can anyone please tell me what the two lines leading to the Oxygen from the secondary carbon are? Why do all the other molecules have just one line leading to them as opposed to this oxygen??

    Awesome vid, btw!!

  11. I always wonder: what happens if you run out of the one particular amino acid you need, but still have plenty of the other 19 floating around?

  12. Thank you for sharing your understanding of biological functions. I have found your presentations incredibly helpful in my college biology class.

  13. kindly help me with this question?a 120 KDa muscle protein is a two stranded coiled coil. estimate the length of the protein molecule?

  14. Doing an online biology class and your 10 minute videos teach me everything better than the 70 minute videos my professors post. Thank you!!! You are a gift to science students everywhere.

  15. have been watching all videos about protein there is in youtube and this guy's the best

  16. Protein is very essential for the growth of the body, to repair damaged tissue, maintaining body functions and also mainly for the immunity system to protect you. Proteins are antibodies that kill bacteria, viruses, and fungi that enter the body. They need to produce hormones that need to the function of the body. Almost all the enzymes used to digest foods are produced from them. They also help to transport various substances and compounds through the blood. As an example, Hemoglobin is a protein that transports oxygen from the lungs to other cells. Therefore it is very important to take a necessary amount of protein from foods daily.
    https://www.tipsforbehealthy.com/healthy-ife/importance-of-having-protein-rich-diet/

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