Full transcript
0:05Hi everybody and welcome to our module
0:07on DNA structure. In this module, we'll
0:09review some basic concepts of DNA that
0:12you should all be familiar with. And
0:13basically the point of this module is to
0:14set the stage so we can talk about the
0:17biochemical synthesis of purines and
0:19primitines. So DNA as you know contains
0:21our genetic code and it's found in the
0:23nucleus of ukarotic cells. It's found in
0:26the cytoplasm of proaryotarotic cells
0:28like bacteria. DNA as you all should
0:30know has two complimentary strands and
0:32I'm drawing a line through the two
0:34strands on this picture of DNA on the
0:36screen. Each strand is made up of a
0:39series of building blocks called a
0:40nucleotide. This is a nucleotide right
0:42here. And a nucleotide contains three
0:44elements. First of all, it has a
0:46phosphate group. Second of all, it has a
0:48ribbo sugar which is right here. And
0:50third, it contains a base. And these are
0:52called nitrogenous bases because they
0:54all contain nitrogen derived from amino
0:56acids. And there are four bases found in
0:59DNA. Adinine and thymine and guanine and
1:02cytosine. And the guanine and cytosine
1:04are complimentary to each other. And so
1:06are the adinine and thymine. So part of
1:08what can be confusing as a medical
1:10student is the vocabulary people use
1:12when they talk about DNA, especially
1:13when you read textbooks. So what I'm
1:14going to do in the next few slides is
1:16just define some terms. We need to know
1:18the difference between a nucleotide and
1:20nucleotide. We need to know what the
1:21nitrogenous bases are. And we need to
1:23know the difference between purines and
1:25primitines.
1:27So DNA, as I showed you before, is a
1:29polymer. It's made up of repeating
1:31units. And those monomer units are
1:33called nucleotides. And like I told you
1:35before, nucleotides have three elements.
1:37They have a pento sugar, which is this
1:39unit right here that I'm circling. They
1:41have a nitrogenous base. The base is not
1:43shown in terms of its chemical
1:44structure, but it would sit right here.
1:46And then finally, they have a phosphate
1:47group. And if you see an O group right
1:50here, then it is a ribboucleotide.
1:53If that O group is removed, as I've
1:55shown you over here, then it is a deoxy
1:57ribboucleotide because the oxygroup has
2:00been removed. So usually people say that
2:03DNA is made up of nucleotides. And when
2:05they say this, they mean it's made up of
2:06repeating structures of a nitrogenous
2:08base, a sugar group, and a phosphate
2:10group. But sometimes you will hear
2:12people use the term nucleioide. And a
2:14nucleotide is the base and sugar with no
2:16phosphate group attached. So if we look
2:18at this picture on the right side of the
2:19screen, you can see that there is a
2:20phosphate group attached right here.
2:22Therefore, this is a nucleotide.
2:24Specifically, it's adenazine mono
2:26phosphate and it's mono because there's
2:28only one phosphate group. If the
2:30phosphate group were removed, this would
2:31be an adenazine nucleioide. And you just
2:34need to know that terminology so you can
2:35understand what you're reading in
2:37textbooks. There are five nitrogenous
2:39bases that are found in nucleotides in
2:42the human body. Three of them have one
2:44ring and those three with one ring are
2:46called primitines and the three
2:47primitines are cytosine and thymine and
2:50uricil and you may know that uricil is
2:52found only in RNA but not in DNA.
2:54Thyonin on the other hand is found in
2:56DNA but not in RNA. Then there are two
2:59additional nitrogenous bases that have
3:01two rings and those are called the
3:02purines and the two purines are adinine
3:04and guanine. Once a nitrogenous base is
3:07attached to a ribbo sugar and a
3:08phosphate group, it becomes a
3:10nucleotide. And the name of the
3:11nucleotide depends on the name of the
3:13base that's attached. So when cytosine
3:15is the base attached, it's called
3:17cytoine. And when thy is attached, it's
3:19called thyodine. And when uricil is
3:20attached, it's called urodine. And all
3:22the perimeitine nucleotides end in d i
3:24ne. For a purine, once the base is
3:27attached, the nucleotide name ends in s
3:29i ne. So when adinine is attached, it's
3:32called adenazine. And when guanine is
3:34attached, it's called guanazine. All of
3:36the nucleotides are synthesized as monof
3:38phosphates. So this means they have a
3:39base like I've shown here and a ribbo
3:41sugar and they have just one phosphate
3:43group. They are then converted to a
3:45triphosphate form. And the reason this
3:47is done is because the triphosphate form
3:49is the form that can be incorporated
3:51into DNA. You need to attach this
3:54phosphate group right here to a hydroxal
3:56group on another DNA monomer on another
3:58nucleotide. In order to do that, you
4:00need three phosphate groups right here.
4:02This makes the reaction favorable so
4:04that these two can be cleaved off and
4:06this one right here can attach to the
4:07hydroxal group on the next DNA
4:09nucleotide.
4:11There is a phenomena in DNA that you
4:13should be familiar with called DNA
4:15methylation. When this occurs, a methyl
4:17group is added to the base cytosine. So
4:20if you look at the bottom of the screen
4:21here on the left side is the structure
4:23of the base cytosine. On the right side
4:25of the screen, I've shown five
4:26methylcytosine and it has a methyl group
4:28added right here and that's called DNA
4:30methylation. it's done to the cytosine
4:32base and this occurs in segments of DNA
4:35where there are repeating CG patterns.
4:37These are called CG islands and what
4:40will happen is the cytoines will be
4:42methylated on both strands. So for
4:43example, if you have a C with a
4:45complimentary G here and then you next
4:47have a G with a complimentary C here,
4:50the cytosine on both strands will become
4:52methylated in these CG islands. And when
4:55this occurs, transcription of the DNA
4:57will become inactivated. This is part of
4:59a bigger subject called epigenetics.
5:01Epigenetics is the study of the way our
5:04genes are turned on or off. So you can
5:06have the same genes as someone else, but
5:08another person may have them turned on
5:09and you may have them turned off. That's
5:11the result of different epigenetics
5:13between you and another person. Human
5:15DNA is about 70% methylated. And the
5:18important thing about this to know is
5:20that if the body finds lots of
5:22unmethylated CG strands floating around,
5:24that can stimulate an immune response
5:26because the innate immune system will
5:28think that all this unmethylated DNA is
5:31probably coming from bacteria and this
5:32can trigger an inflammatory reaction.
5:35Now, although bacterial DNA has less
5:37methylation than ukareotic DNA, there is
5:40some methylation that occurs in the DNA
5:42of bacteria. Bacteria can methylate both
5:44cytosine and adinine. So this makes them
5:46different from ukariats who methylate
5:48predominantly just cytosine. In
5:50addition, methylation serves a different
5:52purpose in bacteria than it does in
5:54humans. In bacteria, methylating DNA
5:57protects the bacteria from viruses,
5:59which you may know are called bacteria
6:00phages. So these phages like to insert
6:03their DNA into the bacteria, but the
6:05bacteria will recognize that that DNA is
6:08not methylated and they will destroy it
6:10using enzymes called endonucleases. This
6:12is part of a broader area of bacterial
6:14research called restriction modification
6:16systems. And these are systems that
6:18bacteria use to prevent their DNA from
6:20becoming modified or restricted. But the
6:23point here to know is that bacterial can
6:25methylate their DNA. And they do this to
6:27protect themselves from infection with
6:29viruses. Now that we've discussed the
6:31molecular structure of DNA, what we're
6:33going to do for the remainder of this
6:34module is talk about how DNA is packaged
6:37so that it will fit in the nucleus. The
6:39DNA that the human body uses is so large
6:41that if it were laid out end to end, it
6:43wouldn't fit inside the nucleus. The way
6:45it fits in the nucleus is by condensing
6:47it in a very specific pattern. So the
6:49first thing we need to talk about is
6:50chromatin. And chromatin is a structure
6:52found in the nucleus of ukarotic cells.
6:55And chromatin consists of DNA plus
6:57proteins. And you may be familiar with
6:59structures called chromosomes. And
7:00chromosomes are units of condensed
7:03chromatin. One of the most important
7:04proteins found inside of chromatin are
7:06the histones. And inside of chromatin,
7:09you can find repeating units of histones
7:12plus DNA which are called nucleosomes.
7:14This is a picture of a nucleosome on the
7:16screen right here. And there are many
7:18many many of these found inside
7:19chromatin. And this is the way that the
7:21DNA condenses so that it can fit inside
7:24of the nucleus. So the histones are
7:26proteins or peptides and they go by
7:28names like H1, H2A, H2B, H3 and H4. All
7:33of the histones contain basic amino
7:35acids and in particular they have a very
7:38high content of two amino acids lysine
7:40and arginine. Lysine and arginine are
7:42both positively charged and this makes
7:44them very good for binding to the
7:47negatively charged phosphate units on
7:49the backbone of DNA. In a nucleosome,
7:51you will find DNA wrapped twice around
7:54four of the histones. So if you look at
7:55this picture on the top of the screen
7:56here, you can see that the DNA
7:58represented by this red strand is
8:00wrapped around four circular histones
8:02H2A, H2B, H3, and H4. It wraps around
8:06these units twice so that there is a
8:08eight histone core made up of two copies
8:10of each of these histones at the top of
8:12the screen here. There's another histone
8:15called H1 which sits outside of the
8:17nucleosome and it is distinct from the
8:19others. It's not in the nucleosome core.
8:22It's larger and it's more basic and it's
8:24important for tying together the beads
8:26on the string. So these octimer of
8:28histones right here often called beads
8:31and they're tied together like beads on
8:32a string by the H1 histones. This is
8:35easier to understand with a picture. So
8:36you know that DNA forms a double helix
8:38and then DNA can wrap around histones to
8:41form a nucleosome and then you can have
8:43a series of those nucleosomes which look
8:45like beads on a string and then the H1
8:48histones will pull all the beads on the
8:50string together to make condensed
8:51chromatin and this is nice and tightly
8:53packaged and it will allow the very very
8:55large human DNA to fit inside of the
8:58nucleus. The place where you will most
9:00often discuss histones in a clinical
9:03context has to do with drug induced
9:05lupus. So drug induced lupus is fever
9:07and joint pains in a rash very similar
9:10to traditional lupus but in this case it
9:12begins after starting a drug and in
9:14patients who develop drug induced lupus
9:16they will have anti-histone antibodies
9:18about 95% of the time contrast this with
9:21patients who have classic lupus they
9:23typically have anti- doublestranded DNA
9:25antibodies and you can see how these two
9:28disorders would look similar because
9:29they both involve auto antibodies
9:31against DNA in the case of drug induced
9:34lupus it's against the histone
9:35molecules. In the case of traditional
9:37lupus, it's against the doublestranded
9:39DNA itself. And there are three classic
9:41drugs you should know for step one that
9:43can cause a drug induced lupus syndrome.
9:45And these are hydraazine, which is a
9:47blood pressure drug, procanomide, which
9:49is an antiarithmic, and isid, which is a
9:51tuberculosis drug. Chromatin can exist
9:54in two forms. The first type is called
9:56heterocchromatin. This is very tightly
9:58condensed chromatin. And when chromatin
10:00is like this, the gene sequences will
10:02not be transcribed. And this varies by
10:04cell. So for example, cardiac cells may
10:07transcribe some genes that kidney cells
10:09do not and vice versa. And remember that
10:11I told you before that DNA methylation
10:13tends to inhibit transcription and you
10:15will find a lot of DNA methylation in
10:18condensed heterocchromatin. The other
10:20type of chromatin is called ukromatin.
10:22is less condensed. Transcription can be
10:24active in ukromatin and there is a
10:27significant amount of acetylation of
10:29histone going on in uk chromatin which
10:31is one of the things that allows the
10:32genes to get turned on. So let's talk
10:35about histone acetilation. Acetilation
10:37means adding an acetal group to a
10:39molecule. In the case of histone
10:41acetilation, we are going to add an
10:42acetal group to lysine. Recall that I
10:44told you that histones contain a lot of
10:46lysine amino acids. This is the chemical
10:48structure of lysine here. This is what
10:50an acetal group looks like. So we are
10:52going to add the cetal group to lysine
10:54and when we do that the chromatin will
10:56relax and transcription can occur. If
10:58you look at this picture on the bottom
10:59of the screen here we have some closed
11:01chromatin on the left side of the
11:03screen. There are enzymes called histone
11:05acetal transferases which will add
11:07acetal groups to lysine. This will relax
11:09the chromatin and allow transcription to
11:11occur. There's also a process called
11:13histone deacetylation and this has the
11:16reverse effect. It packs the chromatin
11:18tightly together and it blocks
11:19transcription. So on this slide, I've
11:21summarized the two epigenetic phenomena
11:23that I think it's important to know for
11:25step one in a way that will hopefully
11:26stick in your mind. So if you have DNA
11:29that wants to be transcribed, if you
11:31acetilate the histones, that will allow
11:33transcription to occur. On the other
11:35hand, if the DNA especially the cytosine
11:37in that DNA gets methylated, then
11:40transcription will not occur. And these
11:41are two epigenetic phenomena. There are
11:43many many more. The field of epigenetics
11:45is very large and diverse. There are
11:47drugs in development called histone
11:48deacetylase inhibitors that have
11:50potential therapeutic effects. You may
11:52one day see them used as anti-cancer
11:54drugs. There are some cancers that have
11:56increased expression of histone
11:58deacetylase enzymes. And so if you
12:00inhibit those, it's thought that you may
12:02limit growth of the tumor. Huntington's
12:04disease is also a disorder where histone
12:06acetylation may play a role. I discussed
12:09this in the neurology modules. It's a
12:11movement disorder where patients have an
12:12abnormal protein called the Huntington
12:14protein. This is a gain of function
12:16disease. There's a mutant protein that
12:18is overactive. And one of the possible
12:20mechanisms by which this Huntington
12:22protein becomes overactive is through
12:24histone deacetylation which silences
12:27genes that should control the Huntington
12:29protein. It's thought that this may lead
12:30to neuron death in the stratum. So there
12:32are histone deacetylase drugs being
12:34studied for treatment of Huntington's
12:36disease. There's a seizure drug called
12:38dalproic acid which has some histone
12:40deacetylase inhibition activity. There's
12:43a nice review article down here on the
12:44bottom of the screen if you want to read
12:46more about these drugs that are in
12:47development.