alexignite/bio_set · Datasets at Hugging Face

text stringlengths 3 503	title stringlengths 10 73
Another procedure, gel filtration Chromatography, in which we separate the proteins based on size.	Analysis of Protein Purification (Part II).txt
And so following that, we extract that sample, we place it into this weld, and this is the band that we get.	Analysis of Protein Purification (Part II).txt
And so this band disappears, other bands disappeared.	Analysis of Protein Purification (Part II).txt
So what that means is we're slowly purifying the protein where we're moving those unwanted proteins as shown by padded increase in the band distribution number.	Analysis of Protein Purification (Part II).txt
So that is what should be shown by this table.	Analysis of Protein Purification (Part II).txt
So let's calculate this box.	Analysis of Protein Purification (Part II).txt
In this box, as always, the specific activity is 85,000 divided by 100.	Analysis of Protein Purification (Part II).txt
The two zeros cancel out and we have 850 divided by one and that gives us 850.	Analysis of Protein Purification (Part II).txt
Now, what about this quantity?	Analysis of Protein Purification (Part II).txt
So to calculate this, we simply take this divided by that.	Analysis of Protein Purification (Part II).txt
So the specific activity of that mixture divided by the original mixture and we get 85.	Analysis of Protein Purification (Part II).txt
So because this divided by this gives us 85.	Analysis of Protein Purification (Part II).txt
And let's use purple for that.	Analysis of Protein Purification (Part II).txt
Okay?	Analysis of Protein Purification (Part II).txt
So what that means is this extracted mixture, following these processes up to this point is 85 times as pure as this initial mixture.	Analysis of Protein Purification (Part II).txt
And finally, let's carry out the final one.	Analysis of Protein Purification (Part II).txt
So in the final step, in step E, we take our extracted mixture of proteins and we expose it to affinity Chromatography.	Analysis of Protein Purification (Part II).txt
And in affinity Chromatography, we separate our proteins based on their specific ability to bind to these special molecules.	Analysis of Protein Purification (Part II).txt
And this usually creates a very high specific activity value because as we know, enzymes only bind to specific substrate to specific molecules.	Analysis of Protein Purification (Part II).txt
So let's see if that's true by taking the extracted mixture and placing it into our last well.	Analysis of Protein Purification (Part II).txt
So what we produce is a band distribution that only contains a single band.	Analysis of Protein Purification (Part II).txt
And what that usually means is we have isolated that protein of interest because this band consists of a protein that has a specific type of mass, a specific type of size.	Analysis of Protein Purification (Part II).txt
Now let's owe and by the way, let's calculate what the yield in this case was.	Analysis of Protein Purification (Part II).txt
To calculate the yield, we follow this equation.	Analysis of Protein Purification (Part II).txt
So this divided by this gives us 85 divided by 200, which is 42.5 divided by 100 multiplied by 100, that gives us a percent of 42.5.	Analysis of Protein Purification (Part II).txt
Okay?	Analysis of Protein Purification (Part II).txt
So let's go back to this step.	Analysis of Protein Purification (Part II).txt
So this basically means that we have successfully isolated that protein.	Analysis of Protein Purification (Part II).txt
We basically have this protein that consists of a single type of mass.	Analysis of Protein Purification (Part II).txt
Now let's see that the specific activity increases and this increases.	Analysis of Protein Purification (Part II).txt
And let's make sure that the yield didn't decrease by too much.	Analysis of Protein Purification (Part II).txt
So if we have at least 30% here, that is a good procedure.	Analysis of Protein Purification (Part II).txt
So let's take a look at E to calculate this.	Analysis of Protein Purification (Part II).txt
We take this divided by two and we get 35,000.	Analysis of Protein Purification (Part II).txt
So we see that in fact, this procedure has a high specific activity.	Analysis of Protein Purification (Part II).txt
And that makes sense because affinity Chromatography separates these enzymes based on their ability to bind to specific enzymes.	Analysis of Protein Purification (Part II).txt
And so in our mixture, when we run our mixture proteins along that column of that affinity chromatography setup, only the protein that we want to study will bind to our beads inside that column, the other proteins will essentially go down because enzymes only bind to specific types of proteins.	Analysis of Protein Purification (Part II).txt
And so that's why this is such a high value, because usually affinity chromatography separates by a very, very large margin.	Analysis of Protein Purification (Part II).txt
Now, what about the purification level?	Analysis of Protein Purification (Part II).txt
So this divided by this gives us 3500.	Analysis of Protein Purification (Part II).txt
And what that means is, after all the procedures that we conducted, the final extracted mixture is 3500 times as pure as that initial sample, and that is a high amount.	Analysis of Protein Purification (Part II).txt
Now, for this set of procedures to actually be good, this yield has to be a high enough yield.	Analysis of Protein Purification (Part II).txt
So let's see what that yield is.	Analysis of Protein Purification (Part II).txt
So we take 70,000 divided by 200,000.	Analysis of Protein Purification (Part II).txt
That gives us 70 divided by 200 or 35 divided by 100.	Analysis of Protein Purification (Part II).txt
We multiply that ratio by 100 and we get 35%.	Analysis of Protein Purification (Part II).txt
And this is a high enough yield.	Analysis of Protein Purification (Part II).txt
So 35% is enough to basically mean we can work with that extracted sample, the protein, to basically study that protein in different ways.	Analysis of Protein Purification (Part II).txt
So these are the five quantities that we have to calculate every time we carry out one of these procedures.	Analysis of Protein Purification (Part II).txt
And then we also normally expose our extracted portion to SDS page to basically help us visualize if our technique is actually working.	Analysis of Protein Purification (Part II).txt
And if we combine these two methods, that gives us a very good idea if the purification technique is working.	Analysis of Protein Purification (Part II).txt
So normally, as we go from A to E, the number of bands should decrease.	Analysis of Protein Purification (Part II).txt
And what that means is we're getting rid of those unwanted proteins and we're focusing in on that protein that we actually want to study.	Analysis of Protein Purification (Part II).txt
And that is confirmed by these measurements because as we purify the sample, the specific activity has to increase and so should our purification level.	Analysis of Protein Purification (Part II).txt
And we also have to keep track of the yield.	Analysis of Protein Purification (Part II).txt
We don't want our yield to drop to a very small amount.	Analysis of Protein Purification (Part II).txt
For example, if following our procedure, this yield would have been, let's say 5%, then this procedure would not have been efficient because at the end, even though we would have had a high purification value, that yield is not enough.	Analysis of Protein Purification (Part II).txt
5% would not have been enough to basically create a mixture protein that is actually usable and workable in a laboratory setting.	Analysis of Protein Purification (Part II).txt
So whenever we're purifying proteins, we have to make sure that the purification level is high and that yield is high enough for us to actually work with that final purified mixture of protein.	Analysis of Protein Purification (Part II).txt
Although DNA molecules contain the genetic information that is needed to build proteins the DNA molecules themselves are not used directly in protein synthesis.	RNA Polymerase .txt
And that's because we want to actually prevent damage to the DNA molecules.	RNA Polymerase .txt
And so what we do is in a process known as transcription we synthesize RNA molecules from DNA molecules.	RNA Polymerase .txt
And what these RNA molecules are they're copies of specific segments of the DNA molecule and these segments usually contain important genes.	RNA Polymerase .txt
So before we can synthesize proteins RNA molecules must be synthesized from DNA molecules in a process known as transcription.	RNA Polymerase .txt
And just like the process of DNA replication involves this protein known as DNA polymerase that catalyzes the formation of a phosphodiastor bond in the process of transcription.	RNA Polymerase .txt
When we form the RNA from the DNA there is a molecule, a protein known as RNA polymerase that catalyzes the formation of the phosphodia Esther Bond.	RNA Polymerase .txt
So RNA polymerase catalyzes the initiation and the elongation of that RNA polynucleotide chain.	RNA Polymerase .txt
And to see what we mean by that, let's take a look at the following diagram.	RNA Polymerase .txt
So in the diagram in this chemical equation we basically describe how this reaction takes place and what RNA polymerase does.	RNA Polymerase .txt
So let's suppose we have an RNA chain and we're extending that RNA chain.	RNA Polymerase .txt
So we're building our RNA molecule.	RNA Polymerase .txt
Now, so far in our RNA molecule we have N number of nucleotides.	RNA Polymerase .txt
And let's suppose we want to add one more nucleotide.	RNA Polymerase .txt
We want to add one more ribonucleotide triphosphate.	RNA Polymerase .txt
Now, what RNA polymerase does and we'll discuss this in much more detail in just a moment what RNA polymerase does is it essentially attaches the ribonucleocide triphosphate onto the RNA molecule to form an RNA molecule that is extended by one nucleotide.	RNA Polymerase .txt
So here we have N number of ribonucleotide triphosphates but here we have N plus one.	RNA Polymerase .txt
And in the process we build this phosphodiastor bond between the ribonucleotide triphosphate and the RNA chain and we release a single pyrophosphate molecule.	RNA Polymerase .txt
So PP stands for a Pyrophosphate and in fact it's the breakdown of the Pyrophosphate that drives this transcription reaction forward as we'll discuss in much more detail when we'll discuss the process of transcription.	RNA Polymerase .txt
So this is the general equation that describes RNA polymerase.	RNA Polymerase .txt
Now, to actually work, what does RNA polymerase actually need?	RNA Polymerase .txt
Well, it needs three different things.	RNA Polymerase .txt
It basically means the building blocks, the ribonucleotide triphosphates and there are four different types.	RNA Polymerase .txt
So we have adenosine five triphosphate we have guanosine five triphosphate we have citadine five prime triphosphate and we have uridine five prime triphosphate.	RNA Polymerase .txt
And these building blocks are needed to actually synthesize and elongate that polynucleotide chain.	RNA Polymerase .txt
Now, number two, it actually needs a preexisting DNA template molecule.	RNA Polymerase .txt
So usually we're dealing with a double stranded DNA molecule and a double stranded DNA molecule works the best.	RNA Polymerase .txt
But in some cases we can also use single stranded DNA molecules as templates.	RNA Polymerase .txt
Now, why do we need a template molecule?	RNA Polymerase .txt
Well, we need the DNA template to basically copy that genetic information.	RNA Polymerase .txt
And it's the template, that DNA template that is used to basically bring those complementary bases to that elongated polynucleotide chain.	RNA Polymerase .txt
So although single stranded DNA molecules work, double stranded DNA molecules are more effective and more common as templates.	RNA Polymerase .txt
So RNA polymerase uses this DNA template to basically build a polynucleotide chain that contains complementary bases as we'll see in just a moment.	RNA Polymerase .txt
And finally, inside the RNA polymerase molecule at the center there is a pocket that can fit a divalent metal atom.	RNA Polymerase .txt
Now, what is a divalent metal atom?	RNA Polymerase .txt
Well, it's a metal atom that can gain a positive charge, a charge of positive two.	RNA Polymerase .txt
So he can lose two electrons and gain a positive charge of two.	RNA Polymerase .txt
And two types of atoms that work in this particular case are magnesium so, Mg and Manganese MN.	RNA Polymerase .txt
And the reason we need this metal atom is because it acts as a cofactor, it increases the efficiency of this enzymes activity.	RNA Polymerase .txt
Now let's take a look at the following diagram that basically describes in detail how that bond is formed.	RNA Polymerase .txt
And notice this phosphodiasta bond is formed in a very similar way to how the phosphodiesta bond is formed when DNA polymerase replicates that DNA molecule.	RNA Polymerase .txt

Another procedure, gel filtration Chromatography, in which we separate the proteins based on size.

Analysis of Protein Purification (Part II).txt

And so following that, we extract that sample, we place it into this weld, and this is the band that we get.

Analysis of Protein Purification (Part II).txt

And so this band disappears, other bands disappeared.

Analysis of Protein Purification (Part II).txt

So what that means is we're slowly purifying the protein where we're moving those unwanted proteins as shown by padded increase in the band distribution number.

Analysis of Protein Purification (Part II).txt

So that is what should be shown by this table.

Analysis of Protein Purification (Part II).txt

So let's calculate this box.

Analysis of Protein Purification (Part II).txt

In this box, as always, the specific activity is 85,000 divided by 100.

Analysis of Protein Purification (Part II).txt

The two zeros cancel out and we have 850 divided by one and that gives us 850.

Analysis of Protein Purification (Part II).txt

Now, what about this quantity?

Analysis of Protein Purification (Part II).txt

So to calculate this, we simply take this divided by that.

Analysis of Protein Purification (Part II).txt

So the specific activity of that mixture divided by the original mixture and we get 85.

Analysis of Protein Purification (Part II).txt

So because this divided by this gives us 85.

Analysis of Protein Purification (Part II).txt

And let's use purple for that.

Analysis of Protein Purification (Part II).txt

Okay?

Analysis of Protein Purification (Part II).txt

So what that means is this extracted mixture, following these processes up to this point is 85 times as pure as this initial mixture.

Analysis of Protein Purification (Part II).txt

And finally, let's carry out the final one.

Analysis of Protein Purification (Part II).txt

So in the final step, in step E, we take our extracted mixture of proteins and we expose it to affinity Chromatography.

Analysis of Protein Purification (Part II).txt

And in affinity Chromatography, we separate our proteins based on their specific ability to bind to these special molecules.

Analysis of Protein Purification (Part II).txt

And this usually creates a very high specific activity value because as we know, enzymes only bind to specific substrate to specific molecules.

Analysis of Protein Purification (Part II).txt

So let's see if that's true by taking the extracted mixture and placing it into our last well.

Analysis of Protein Purification (Part II).txt

So what we produce is a band distribution that only contains a single band.

Analysis of Protein Purification (Part II).txt

And what that usually means is we have isolated that protein of interest because this band consists of a protein that has a specific type of mass, a specific type of size.

Analysis of Protein Purification (Part II).txt

Now let's owe and by the way, let's calculate what the yield in this case was.

Analysis of Protein Purification (Part II).txt

To calculate the yield, we follow this equation.

Analysis of Protein Purification (Part II).txt

So this divided by this gives us 85 divided by 200, which is 42.5 divided by 100 multiplied by 100, that gives us a percent of 42.5.

Analysis of Protein Purification (Part II).txt

Okay?

Analysis of Protein Purification (Part II).txt

So let's go back to this step.

Analysis of Protein Purification (Part II).txt

So this basically means that we have successfully isolated that protein.

Analysis of Protein Purification (Part II).txt

We basically have this protein that consists of a single type of mass.

Analysis of Protein Purification (Part II).txt

Now let's see that the specific activity increases and this increases.

Analysis of Protein Purification (Part II).txt

And let's make sure that the yield didn't decrease by too much.

Analysis of Protein Purification (Part II).txt

So if we have at least 30% here, that is a good procedure.

Analysis of Protein Purification (Part II).txt

So let's take a look at E to calculate this.

Analysis of Protein Purification (Part II).txt

We take this divided by two and we get 35,000.

Analysis of Protein Purification (Part II).txt

So we see that in fact, this procedure has a high specific activity.

Analysis of Protein Purification (Part II).txt

And that makes sense because affinity Chromatography separates these enzymes based on their ability to bind to specific enzymes.

Analysis of Protein Purification (Part II).txt

And so in our mixture, when we run our mixture proteins along that column of that affinity chromatography setup, only the protein that we want to study will bind to our beads inside that column, the other proteins will essentially go down because enzymes only bind to specific types of proteins.

Analysis of Protein Purification (Part II).txt

And so that's why this is such a high value, because usually affinity chromatography separates by a very, very large margin.

Analysis of Protein Purification (Part II).txt

Now, what about the purification level?

Analysis of Protein Purification (Part II).txt

So this divided by this gives us 3500.

Analysis of Protein Purification (Part II).txt

And what that means is, after all the procedures that we conducted, the final extracted mixture is 3500 times as pure as that initial sample, and that is a high amount.

Analysis of Protein Purification (Part II).txt

Now, for this set of procedures to actually be good, this yield has to be a high enough yield.

Analysis of Protein Purification (Part II).txt

So let's see what that yield is.

Analysis of Protein Purification (Part II).txt

So we take 70,000 divided by 200,000.

Analysis of Protein Purification (Part II).txt

That gives us 70 divided by 200 or 35 divided by 100.

Analysis of Protein Purification (Part II).txt

We multiply that ratio by 100 and we get 35%.

Analysis of Protein Purification (Part II).txt

And this is a high enough yield.

Analysis of Protein Purification (Part II).txt

So 35% is enough to basically mean we can work with that extracted sample, the protein, to basically study that protein in different ways.

Analysis of Protein Purification (Part II).txt

So these are the five quantities that we have to calculate every time we carry out one of these procedures.

Analysis of Protein Purification (Part II).txt

And then we also normally expose our extracted portion to SDS page to basically help us visualize if our technique is actually working.

Analysis of Protein Purification (Part II).txt

And if we combine these two methods, that gives us a very good idea if the purification technique is working.

Analysis of Protein Purification (Part II).txt

So normally, as we go from A to E, the number of bands should decrease.

Analysis of Protein Purification (Part II).txt

And what that means is we're getting rid of those unwanted proteins and we're focusing in on that protein that we actually want to study.

Analysis of Protein Purification (Part II).txt

And that is confirmed by these measurements because as we purify the sample, the specific activity has to increase and so should our purification level.

Analysis of Protein Purification (Part II).txt

And we also have to keep track of the yield.

Analysis of Protein Purification (Part II).txt

We don't want our yield to drop to a very small amount.

Analysis of Protein Purification (Part II).txt

For example, if following our procedure, this yield would have been, let's say 5%, then this procedure would not have been efficient because at the end, even though we would have had a high purification value, that yield is not enough.

Analysis of Protein Purification (Part II).txt

5% would not have been enough to basically create a mixture protein that is actually usable and workable in a laboratory setting.

Analysis of Protein Purification (Part II).txt

So whenever we're purifying proteins, we have to make sure that the purification level is high and that yield is high enough for us to actually work with that final purified mixture of protein.

Analysis of Protein Purification (Part II).txt

Although DNA molecules contain the genetic information that is needed to build proteins the DNA molecules themselves are not used directly in protein synthesis.

RNA Polymerase .txt

And that's because we want to actually prevent damage to the DNA molecules.

RNA Polymerase .txt

And so what we do is in a process known as transcription we synthesize RNA molecules from DNA molecules.

RNA Polymerase .txt

And what these RNA molecules are they're copies of specific segments of the DNA molecule and these segments usually contain important genes.

RNA Polymerase .txt

So before we can synthesize proteins RNA molecules must be synthesized from DNA molecules in a process known as transcription.

RNA Polymerase .txt

And just like the process of DNA replication involves this protein known as DNA polymerase that catalyzes the formation of a phosphodiastor bond in the process of transcription.

RNA Polymerase .txt

When we form the RNA from the DNA there is a molecule, a protein known as RNA polymerase that catalyzes the formation of the phosphodia Esther Bond.

RNA Polymerase .txt

So RNA polymerase catalyzes the initiation and the elongation of that RNA polynucleotide chain.

RNA Polymerase .txt

And to see what we mean by that, let's take a look at the following diagram.

RNA Polymerase .txt

So in the diagram in this chemical equation we basically describe how this reaction takes place and what RNA polymerase does.

RNA Polymerase .txt

So let's suppose we have an RNA chain and we're extending that RNA chain.

RNA Polymerase .txt

So we're building our RNA molecule.

RNA Polymerase .txt

Now, so far in our RNA molecule we have N number of nucleotides.

RNA Polymerase .txt

And let's suppose we want to add one more nucleotide.

RNA Polymerase .txt

We want to add one more ribonucleotide triphosphate.

RNA Polymerase .txt

Now, what RNA polymerase does and we'll discuss this in much more detail in just a moment what RNA polymerase does is it essentially attaches the ribonucleocide triphosphate onto the RNA molecule to form an RNA molecule that is extended by one nucleotide.

RNA Polymerase .txt

So here we have N number of ribonucleotide triphosphates but here we have N plus one.

RNA Polymerase .txt

And in the process we build this phosphodiastor bond between the ribonucleotide triphosphate and the RNA chain and we release a single pyrophosphate molecule.

RNA Polymerase .txt

So PP stands for a Pyrophosphate and in fact it's the breakdown of the Pyrophosphate that drives this transcription reaction forward as we'll discuss in much more detail when we'll discuss the process of transcription.

RNA Polymerase .txt

So this is the general equation that describes RNA polymerase.

RNA Polymerase .txt

Now, to actually work, what does RNA polymerase actually need?

RNA Polymerase .txt

Well, it needs three different things.

RNA Polymerase .txt

It basically means the building blocks, the ribonucleotide triphosphates and there are four different types.

RNA Polymerase .txt

So we have adenosine five triphosphate we have guanosine five triphosphate we have citadine five prime triphosphate and we have uridine five prime triphosphate.

RNA Polymerase .txt

And these building blocks are needed to actually synthesize and elongate that polynucleotide chain.

RNA Polymerase .txt

Now, number two, it actually needs a preexisting DNA template molecule.

RNA Polymerase .txt

So usually we're dealing with a double stranded DNA molecule and a double stranded DNA molecule works the best.

RNA Polymerase .txt

But in some cases we can also use single stranded DNA molecules as templates.

RNA Polymerase .txt

Now, why do we need a template molecule?

RNA Polymerase .txt

Well, we need the DNA template to basically copy that genetic information.

RNA Polymerase .txt

And it's the template, that DNA template that is used to basically bring those complementary bases to that elongated polynucleotide chain.

RNA Polymerase .txt

So although single stranded DNA molecules work, double stranded DNA molecules are more effective and more common as templates.

RNA Polymerase .txt

So RNA polymerase uses this DNA template to basically build a polynucleotide chain that contains complementary bases as we'll see in just a moment.

RNA Polymerase .txt

And finally, inside the RNA polymerase molecule at the center there is a pocket that can fit a divalent metal atom.

RNA Polymerase .txt

Now, what is a divalent metal atom?

RNA Polymerase .txt

Well, it's a metal atom that can gain a positive charge, a charge of positive two.

RNA Polymerase .txt

So he can lose two electrons and gain a positive charge of two.

RNA Polymerase .txt

And two types of atoms that work in this particular case are magnesium so, Mg and Manganese MN.

RNA Polymerase .txt

And the reason we need this metal atom is because it acts as a cofactor, it increases the efficiency of this enzymes activity.

RNA Polymerase .txt

Now let's take a look at the following diagram that basically describes in detail how that bond is formed.

RNA Polymerase .txt

And notice this phosphodiasta bond is formed in a very similar way to how the phosphodiesta bond is formed when DNA polymerase replicates that DNA molecule.

RNA Polymerase .txt