DarthJudie/biosetpart1 · Datasets at Hugging Face

title stringlengths 7 100	text stringlengths 1 16k
AP Bio Macromolecules - Part 2	And then they have oftentimes like a hydrogen off one side, but then they have this R group.
AP Bio Macromolecules - Part 2	So they've got this one other piece that comes off and this piece ultimately is different for each amino acid.
AP Bio Macromolecules - Part 2	And this R group can have different characteristics.
AP Bio Macromolecules - Part 2	That R group might be polar in one type of amino acid.
AP Bio Macromolecules - Part 2	It could be non-polar in another.
AP Bio Macromolecules - Part 2	It could be acidic.
AP Bio Macromolecules - Part 2	It could be basic.
AP Bio Macromolecules - Part 2	It can have these different characteristics that can help give that a little bit of that characteristic to the protein as a whole that's being made.
AP Bio Macromolecules - Part 2	And so if a protein being made has a lot of polar amino acids in R groups, it's likely that that protein is going to be much more polar overall.
AP Bio Macromolecules - Part 2	And so it can be used in certain areas where you need them to be polar.
AP Bio Macromolecules - Part 2	So these R groups are critical and the fact that there's 20 different amino acids to choose from is critical in giving us a diversity.
AP Bio Macromolecules - Part 2	There's a tremendous, insane it seems like, number of proteins that can be made.
AP Bio Macromolecules - Part 2	Just a simple thing, if you have a seven digit phone number, you've got ten options for each number, zero to nine.
AP Bio Macromolecules - Part 2	That gives you a million different possible phone numbers if I've done my math there correctly.
AP Bio Macromolecules - Part 2	Ten to the seventh.
AP Bio Macromolecules - Part 2	Ten is the options that you have overall for each slot and seven slots.
AP Bio Macromolecules - Part 2	So if you figure that many proteins can be thousands of amino acids long, that's like a phone number that goes on for like 2,000 digits.
AP Bio Macromolecules - Part 2	And for each one slot, where normally in our phone number we can put a zero through nine, you'd have 20 different options.
AP Bio Macromolecules - Part 2	So there's this nearly, I don't want to say infinite quite, but there's this ridiculously high amount of proteins that could be made even if you cap off proteins at only say 5,000 amino acids.
AP Bio Macromolecules - Part 2	Obviously if you go on forever, a number of amino acids, you could have an infinite amount.
AP Bio Macromolecules - Part 2	But realistically, biologically, there's just an insane number which allows proteins to do so much.
AP Bio Macromolecules - Part 2	Because we have so many options as we are building proteins and mutations occur and allow changes in the proteins, we can get new proteins that serve different functions.
AP Bio Macromolecules - Part 2	In some cases, better functions that allow us to develop new characteristics or better versions of the old characteristic, as well as worse ones, although those people typically die off and take their little screw up with them that didn't turn out so hot.
AP Bio Macromolecules - Part 2	Now in addition to having so many different options as far as the order of amino acids and which amino acids you choose, there's also going to be levels of structure we're going to talk about.
AP Bio Macromolecules - Part 2	Now the first level is pretty straightforward.
AP Bio Macromolecules - Part 2	It's primary structure, primary for one, and that's where we actually just bind these different amino acids together.
AP Bio Macromolecules - Part 2	Sometimes they'll call that a peptide bond, just a covalent bond, and so you'll just bind them together more or less in a linear fashion.
AP Bio Macromolecules - Part 2	We see they can bend and weave a bit, but we're sticking them together bit by bit, kind of like you're putting beads in a necklace to get this long chain.
AP Bio Macromolecules - Part 2	That's our primary structure.
AP Bio Macromolecules - Part 2	And so most of our proteins are going to have a unique amino acid sequence.
AP Bio Macromolecules - Part 2	So they have a specific order of amino acids and a specific total length overall.
AP Bio Macromolecules - Part 2	Now if we mess with that, if we do some substitutions, I won't really get, later on we'll talk about, in much later chapters, deletions and things like that.
AP Bio Macromolecules - Part 2	But if you just do small changes even, you can get different structures, you can get where they're affected.
AP Bio Macromolecules - Part 2	And so for instance, if we mess with hemoglobin by swapping out just a little bit as far as amino acids go, you can ultimately end up with your blood cells changing overall in their shape.
AP Bio Macromolecules - Part 2	Hemoglobin is one of the proteins they have, and it makes them sickle shaped.
AP Bio Macromolecules - Part 2	And so it's not surprising we call people who have that, we call them sufferers of sickle cell anemia.
AP Bio Macromolecules - Part 2	And that's because these blood cells don't really do their job as well.
AP Bio Macromolecules - Part 2	They tend to die off, they tend to clot.
AP Bio Macromolecules - Part 2	And so individuals tend to get anemia, low blood cells, low red blood cells, and they tend to get clots, which can lead to organ failure, pain, and a bunch of things that are not positive.
AP Bio Macromolecules - Part 2	So people that have two of these alleles get sickle cell anemia, and that's a very bad thing to have.
AP Bio Macromolecules - Part 2	It does help prevent you getting malaria, but if you get two of these alleles, the change in the protein structure can be a very negative thing.
AP Bio Macromolecules - Part 2	And so this just illustrates that even small changes in exactly which amino acids you have can have an effect in what you get and what that protein is capable of doing.
AP Bio Macromolecules - Part 2	Oftentimes negative, sometimes it just doesn't matter.
AP Bio Macromolecules - Part 2	It's a similar enough amino acid that even though you change the amino acids, it's still polar enough that you get something similar.
AP Bio Macromolecules - Part 2	And occasionally you might get something better.
AP Bio Macromolecules - Part 2	Secondary structure is where we take this longer chain and we start to kind of fold it up and hydrogen bond it to itself, which will allow it to ultimately get into these different structures, these different higher level structures.
AP Bio Macromolecules - Part 2	And the common ones we'll see are these folded sheet looking things called pleated sheets or beta pleated sheets.
AP Bio Macromolecules - Part 2	And we'll see where it twists, where you get this kind of helical shape, and we call that an alpha helix.
AP Bio Macromolecules - Part 2	So those are the two secondary structures that we'll talk about.
AP Bio Macromolecules - Part 2	And just remember it's due to hydrogen bonds, and we're going to get these helixes and these folded sheets, these pleated sheets.
AP Bio Macromolecules - Part 2	And then those secondary structures, whoops, those, how did I lose one here?
AP Bio Macromolecules - Part 2	Oh, I'm out of order.
AP Bio Macromolecules - Part 2	These secondary structures can ultimately go through and develop into tertiary structures.
AP Bio Macromolecules - Part 2	And what the tertiary structure is, is this is going to be a third level structure where these alpha helixes and these beta pleated sheets and these earlier levels of structure can start to interact with each other.
AP Bio Macromolecules - Part 2	So there are groups start to get near one another close enough sometimes that if they're both nonpolar, they kind of huddle together, just like the lipids would do to form a bilayer.
AP Bio Macromolecules - Part 2	And that's because they're both hydrophobic.
AP Bio Macromolecules - Part 2	So you can get what we call hydrophobic interactions.
AP Bio Macromolecules - Part 2	You can get where if they both have a sulfur that's kind of near each other, those sulfurs can bind and form a disulfide bridge.
AP Bio Macromolecules - Part 2	That's an actual covalent bond.
AP Bio Macromolecules - Part 2	You can get hydrogen bonds.
AP Bio Macromolecules - Part 2	And in some cases, if you've got a carboxyl group, they'll kick off the H. So they'll essentially lose an H plus to become COO minus.
AP Bio Macromolecules - Part 2	And you'll have NH3 will oftentimes grab hold of an extra H plus.
AP Bio Macromolecules - Part 2	So essentially it gains one to become NH3 plus.
AP Bio Macromolecules - Part 2	And so these guys can actually get together, for instance, and get this ionic bond if they get close enough because opposites attract.
AP Bio Macromolecules - Part 2	And overall what this gives us then is all this comes together to give us this complex 3D conformation or shape.
AP Bio Macromolecules - Part 2	And this 3D shape of a protein, or in this case it's oftentimes considered a polypeptide at this point, because it's not quite as big as most of our proteins are, that's going to be considered critical because the shape of a protein determines its function.
AP Bio Macromolecules - Part 2	If we change its shape or its conformation, we change the ability for it to function.
AP Bio Macromolecules - Part 2	In most cases, if something stops functioning and that's a vital function, you're screwed.
AP Bio Macromolecules - Part 2	In some cases, it's not so important.
AP Bio Macromolecules - Part 2	And so if that one changes its function, it's not as big of a deal.
AP Bio Macromolecules - Part 2	So you can get new traits.
AP Bio Macromolecules - Part 2	So this could be something where the pigments in our eyes can mutate and become blue instead of brown or green.
AP Bio Macromolecules - Part 2	And ultimately that really didn't impact as much.
AP Bio Macromolecules - Part 2	So you see that mutation can continue because nothing weeds it out.
AP Bio Macromolecules - Part 2	And so these things will occur, but this 3D shape is critical to enzymes, to all proteins, and exactly how they function.
AP Bio Macromolecules - Part 2	And there is one, I'm going to jump back here to get there, there is one more level that you can have.
AP Bio Macromolecules - Part 2	Some proteins pretty much end at tertiary.
AP Bio Macromolecules - Part 2	They get one giant polypeptide, which ends up being a protein.
AP Bio Macromolecules - Part 2	But a lot of proteins are actually composed of multiple polypeptides.
AP Bio Macromolecules - Part 2	And so we call that the quaternary structure, where they take this chain of amino acids, they hydrogen bond it into these shapes, they ultimately bind those together, these 3D shapes.
AP Bio Macromolecules - Part 2	But then many of them will actually take multiple of these polypeptide subunits, and then they'll stick them together to make this kind of one big protein.
AP Bio Macromolecules - Part 2	So for instance, hemoglobin, which is what you see here, it's comprised of four different subunits that all stick together.
AP Bio Macromolecules - Part 2	And so because it has four of these polypeptides, these four subunits, it has a quaternary structure to make the protein.
AP Bio Macromolecules - Part 2	Collagen is not much different, they just kind of weave together in that one because it's a longer overall protein.
AP Bio Macromolecules - Part 2	But both of them have quaternary structure because they have multiple polypeptides in one protein.
AP Bio Macromolecules - Part 2	That's very common to find.
AP Bio Macromolecules - Part 2	Nucleic acids.
AP Bio Macromolecules - Part 2	This one, there's two big guys that you should know, DNA and RNA.
AP Bio Macromolecules - Part 2	And that shouldn't be too much of a surprise, seeing as they both have nucleic acid in their name, that's the NA, so it's deoxyribonucleic acid and ribonucleic acid.
AP Bio Macromolecules - Part 2	We'll talk in a slide coming up as to why they differ in that first word, first prefix, if you will.
AP Bio Macromolecules - Part 2	Now these will both be critical.
AP Bio Macromolecules - Part 2	Just like I said, proteins are essential for most things to live, living-wise, or at least anything remotely complex, even like a bacteria, as we know it now to live.
AP Bio Macromolecules - Part 2	DNA and RNA are probably just as important because DNA contains the storage, the information that gets copied to RNA, right?
AP Bio Macromolecules - Part 2	That way the DNA is protected.
AP Bio Macromolecules - Part 2	The RNA is then used, and you can see tRNA, mRNA, and the ribosome itself is rRNA.
AP Bio Macromolecules - Part 2	They are then used to make proteins.
AP Bio Macromolecules - Part 2	So the proteins that you can make, the way that we do this, is encoded in your DNA and uses RNA to allow it to be produced.
AP Bio Macromolecules - Part 2	So if protein is critically important, these both have to be critically important as well because they determine the proteins.
AP Bio Macromolecules - Part 2	And polynucleotide, because nucleotides are the monomer, we'll oftentimes, or in some cases you might at least see it referred to as a polynucleotide instead of just saying nucleic acid, just terminology.
AP Bio Macromolecules - Part 2	Okay, the nucleotide is the monomer.

AP Bio Macromolecules - Part 2

And then they have oftentimes like a hydrogen off one side, but then they have this R group.

AP Bio Macromolecules - Part 2

So they've got this one other piece that comes off and this piece ultimately is different for each amino acid.

AP Bio Macromolecules - Part 2

And this R group can have different characteristics.

AP Bio Macromolecules - Part 2

That R group might be polar in one type of amino acid.

AP Bio Macromolecules - Part 2

It could be non-polar in another.

AP Bio Macromolecules - Part 2

It could be acidic.

AP Bio Macromolecules - Part 2

It could be basic.

AP Bio Macromolecules - Part 2

It can have these different characteristics that can help give that a little bit of that characteristic to the protein as a whole that's being made.

AP Bio Macromolecules - Part 2

And so if a protein being made has a lot of polar amino acids in R groups, it's likely that that protein is going to be much more polar overall.

AP Bio Macromolecules - Part 2

And so it can be used in certain areas where you need them to be polar.

AP Bio Macromolecules - Part 2

So these R groups are critical and the fact that there's 20 different amino acids to choose from is critical in giving us a diversity.

AP Bio Macromolecules - Part 2

There's a tremendous, insane it seems like, number of proteins that can be made.

AP Bio Macromolecules - Part 2

Just a simple thing, if you have a seven digit phone number, you've got ten options for each number, zero to nine.

AP Bio Macromolecules - Part 2

That gives you a million different possible phone numbers if I've done my math there correctly.

AP Bio Macromolecules - Part 2

Ten to the seventh.

AP Bio Macromolecules - Part 2

Ten is the options that you have overall for each slot and seven slots.

AP Bio Macromolecules - Part 2

So if you figure that many proteins can be thousands of amino acids long, that's like a phone number that goes on for like 2,000 digits.

AP Bio Macromolecules - Part 2

And for each one slot, where normally in our phone number we can put a zero through nine, you'd have 20 different options.

AP Bio Macromolecules - Part 2

So there's this nearly, I don't want to say infinite quite, but there's this ridiculously high amount of proteins that could be made even if you cap off proteins at only say 5,000 amino acids.

AP Bio Macromolecules - Part 2

Obviously if you go on forever, a number of amino acids, you could have an infinite amount.

AP Bio Macromolecules - Part 2

But realistically, biologically, there's just an insane number which allows proteins to do so much.

AP Bio Macromolecules - Part 2

Because we have so many options as we are building proteins and mutations occur and allow changes in the proteins, we can get new proteins that serve different functions.

AP Bio Macromolecules - Part 2

In some cases, better functions that allow us to develop new characteristics or better versions of the old characteristic, as well as worse ones, although those people typically die off and take their little screw up with them that didn't turn out so hot.

AP Bio Macromolecules - Part 2

Now in addition to having so many different options as far as the order of amino acids and which amino acids you choose, there's also going to be levels of structure we're going to talk about.

AP Bio Macromolecules - Part 2

Now the first level is pretty straightforward.

AP Bio Macromolecules - Part 2

It's primary structure, primary for one, and that's where we actually just bind these different amino acids together.

AP Bio Macromolecules - Part 2

Sometimes they'll call that a peptide bond, just a covalent bond, and so you'll just bind them together more or less in a linear fashion.

AP Bio Macromolecules - Part 2

We see they can bend and weave a bit, but we're sticking them together bit by bit, kind of like you're putting beads in a necklace to get this long chain.

AP Bio Macromolecules - Part 2

That's our primary structure.

AP Bio Macromolecules - Part 2

And so most of our proteins are going to have a unique amino acid sequence.

AP Bio Macromolecules - Part 2

So they have a specific order of amino acids and a specific total length overall.

AP Bio Macromolecules - Part 2

Now if we mess with that, if we do some substitutions, I won't really get, later on we'll talk about, in much later chapters, deletions and things like that.

AP Bio Macromolecules - Part 2

But if you just do small changes even, you can get different structures, you can get where they're affected.

AP Bio Macromolecules - Part 2

And so for instance, if we mess with hemoglobin by swapping out just a little bit as far as amino acids go, you can ultimately end up with your blood cells changing overall in their shape.

AP Bio Macromolecules - Part 2

Hemoglobin is one of the proteins they have, and it makes them sickle shaped.

AP Bio Macromolecules - Part 2

And so it's not surprising we call people who have that, we call them sufferers of sickle cell anemia.

AP Bio Macromolecules - Part 2

And that's because these blood cells don't really do their job as well.

AP Bio Macromolecules - Part 2

They tend to die off, they tend to clot.

AP Bio Macromolecules - Part 2

And so individuals tend to get anemia, low blood cells, low red blood cells, and they tend to get clots, which can lead to organ failure, pain, and a bunch of things that are not positive.

AP Bio Macromolecules - Part 2

So people that have two of these alleles get sickle cell anemia, and that's a very bad thing to have.

AP Bio Macromolecules - Part 2

It does help prevent you getting malaria, but if you get two of these alleles, the change in the protein structure can be a very negative thing.

AP Bio Macromolecules - Part 2

And so this just illustrates that even small changes in exactly which amino acids you have can have an effect in what you get and what that protein is capable of doing.

AP Bio Macromolecules - Part 2

Oftentimes negative, sometimes it just doesn't matter.

AP Bio Macromolecules - Part 2

It's a similar enough amino acid that even though you change the amino acids, it's still polar enough that you get something similar.

AP Bio Macromolecules - Part 2

And occasionally you might get something better.

AP Bio Macromolecules - Part 2

Secondary structure is where we take this longer chain and we start to kind of fold it up and hydrogen bond it to itself, which will allow it to ultimately get into these different structures, these different higher level structures.

AP Bio Macromolecules - Part 2

And the common ones we'll see are these folded sheet looking things called pleated sheets or beta pleated sheets.

AP Bio Macromolecules - Part 2

And we'll see where it twists, where you get this kind of helical shape, and we call that an alpha helix.

AP Bio Macromolecules - Part 2

So those are the two secondary structures that we'll talk about.

AP Bio Macromolecules - Part 2

And just remember it's due to hydrogen bonds, and we're going to get these helixes and these folded sheets, these pleated sheets.

AP Bio Macromolecules - Part 2

And then those secondary structures, whoops, those, how did I lose one here?

AP Bio Macromolecules - Part 2

Oh, I'm out of order.

AP Bio Macromolecules - Part 2

These secondary structures can ultimately go through and develop into tertiary structures.

AP Bio Macromolecules - Part 2

And what the tertiary structure is, is this is going to be a third level structure where these alpha helixes and these beta pleated sheets and these earlier levels of structure can start to interact with each other.

AP Bio Macromolecules - Part 2

So there are groups start to get near one another close enough sometimes that if they're both nonpolar, they kind of huddle together, just like the lipids would do to form a bilayer.

AP Bio Macromolecules - Part 2

And that's because they're both hydrophobic.

AP Bio Macromolecules - Part 2

So you can get what we call hydrophobic interactions.

AP Bio Macromolecules - Part 2

You can get where if they both have a sulfur that's kind of near each other, those sulfurs can bind and form a disulfide bridge.

AP Bio Macromolecules - Part 2

That's an actual covalent bond.

AP Bio Macromolecules - Part 2

You can get hydrogen bonds.

AP Bio Macromolecules - Part 2

And in some cases, if you've got a carboxyl group, they'll kick off the H. So they'll essentially lose an H plus to become COO minus.

AP Bio Macromolecules - Part 2

And you'll have NH3 will oftentimes grab hold of an extra H plus.

AP Bio Macromolecules - Part 2

So essentially it gains one to become NH3 plus.

AP Bio Macromolecules - Part 2

And so these guys can actually get together, for instance, and get this ionic bond if they get close enough because opposites attract.

AP Bio Macromolecules - Part 2

And overall what this gives us then is all this comes together to give us this complex 3D conformation or shape.

AP Bio Macromolecules - Part 2

And this 3D shape of a protein, or in this case it's oftentimes considered a polypeptide at this point, because it's not quite as big as most of our proteins are, that's going to be considered critical because the shape of a protein determines its function.

AP Bio Macromolecules - Part 2

If we change its shape or its conformation, we change the ability for it to function.

AP Bio Macromolecules - Part 2

In most cases, if something stops functioning and that's a vital function, you're screwed.

AP Bio Macromolecules - Part 2

In some cases, it's not so important.

AP Bio Macromolecules - Part 2

And so if that one changes its function, it's not as big of a deal.

AP Bio Macromolecules - Part 2

So you can get new traits.

AP Bio Macromolecules - Part 2

So this could be something where the pigments in our eyes can mutate and become blue instead of brown or green.

AP Bio Macromolecules - Part 2

And ultimately that really didn't impact as much.

AP Bio Macromolecules - Part 2

So you see that mutation can continue because nothing weeds it out.

AP Bio Macromolecules - Part 2

And so these things will occur, but this 3D shape is critical to enzymes, to all proteins, and exactly how they function.

AP Bio Macromolecules - Part 2

And there is one, I'm going to jump back here to get there, there is one more level that you can have.

AP Bio Macromolecules - Part 2

Some proteins pretty much end at tertiary.

AP Bio Macromolecules - Part 2

They get one giant polypeptide, which ends up being a protein.

AP Bio Macromolecules - Part 2

But a lot of proteins are actually composed of multiple polypeptides.

AP Bio Macromolecules - Part 2

And so we call that the quaternary structure, where they take this chain of amino acids, they hydrogen bond it into these shapes, they ultimately bind those together, these 3D shapes.

AP Bio Macromolecules - Part 2

But then many of them will actually take multiple of these polypeptide subunits, and then they'll stick them together to make this kind of one big protein.

AP Bio Macromolecules - Part 2

So for instance, hemoglobin, which is what you see here, it's comprised of four different subunits that all stick together.

AP Bio Macromolecules - Part 2

And so because it has four of these polypeptides, these four subunits, it has a quaternary structure to make the protein.

AP Bio Macromolecules - Part 2

Collagen is not much different, they just kind of weave together in that one because it's a longer overall protein.

AP Bio Macromolecules - Part 2

But both of them have quaternary structure because they have multiple polypeptides in one protein.

AP Bio Macromolecules - Part 2

That's very common to find.

AP Bio Macromolecules - Part 2

Nucleic acids.

AP Bio Macromolecules - Part 2

This one, there's two big guys that you should know, DNA and RNA.

AP Bio Macromolecules - Part 2

And that shouldn't be too much of a surprise, seeing as they both have nucleic acid in their name, that's the NA, so it's deoxyribonucleic acid and ribonucleic acid.

AP Bio Macromolecules - Part 2

We'll talk in a slide coming up as to why they differ in that first word, first prefix, if you will.

AP Bio Macromolecules - Part 2

Now these will both be critical.

AP Bio Macromolecules - Part 2

Just like I said, proteins are essential for most things to live, living-wise, or at least anything remotely complex, even like a bacteria, as we know it now to live.

AP Bio Macromolecules - Part 2

DNA and RNA are probably just as important because DNA contains the storage, the information that gets copied to RNA, right?

AP Bio Macromolecules - Part 2

That way the DNA is protected.

AP Bio Macromolecules - Part 2

The RNA is then used, and you can see tRNA, mRNA, and the ribosome itself is rRNA.

AP Bio Macromolecules - Part 2

They are then used to make proteins.

AP Bio Macromolecules - Part 2

So the proteins that you can make, the way that we do this, is encoded in your DNA and uses RNA to allow it to be produced.

AP Bio Macromolecules - Part 2

So if protein is critically important, these both have to be critically important as well because they determine the proteins.

AP Bio Macromolecules - Part 2

And polynucleotide, because nucleotides are the monomer, we'll oftentimes, or in some cases you might at least see it referred to as a polynucleotide instead of just saying nucleic acid, just terminology.

AP Bio Macromolecules - Part 2

Okay, the nucleotide is the monomer.