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Nucleic acid structure 1

Created by Efrat Bruck.

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  • leafers ultimate style avatar for user Justin
    Would higher occurrences of pyrimidine or purine bases have any increased chance on mutations/coding errors?
    (7 votes)
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    • aqualine ultimate style avatar for user Alessandro.M.Rosa
      You would want to look up the concept of Mutation Hotspot Regions. Basically there are sequences in the Genome that are statistically more susceptible to mutations than other areas.

      As for coding errors, I am not sure if you are referring to errors in replication, transcription, or translation. The short answer is that yes, there are some areas where the DNA and RNA polymerases can stall or skip, introducing the possibility of a base change. When it is in DNA, the DNA repair mechanisms will need to resolve this. For RNA, it is likely just an RNA that will not get translated or if it does make it to a ribosome will lead to a non-fuctional protein, depending on what position the error is in and if it causes an amino acid change.
      (7 votes)
  • blobby green style avatar for user Martin
    I thought that in eukaryotes, when the mRNA is processed in the nucleus before going to the cytoplasm, the noncoding regions, or "introns" were removed from the sequence. Is this true? If so, why are there noncoding regions included in the sequence shown here for eukaryotes?
    (2 votes)
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  • duskpin ultimate style avatar for user invisible.anomaly
    I'm an AP Bio student studying protein synthesis, and this video raised a question: if the C-G bond is stronger due to the three H-bonds, is this related at all to the reason for the 5' guanine cap during mRNA processing? (I realize the mRNA is a single strand, but I'm curious if guanine's ability to form three bonds has anything to do with the preference of guanine over the other nucleotides.) If not, then why does guanine do a good job of preventing RNA degradation in the cytoplasm?
    (2 votes)
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    • duskpin ultimate style avatar for user cx1
      As you mentioned mRNA is single stranded. The 5' guanine cap refers to the linkage between the 5' end of mRNA (ribose) and a 5'end of GTP not GC bonds. Therefore making a 5'-5' linkage between the molecules. The purpose of this is to prevent degradation via exonuclease and it also aids in ribosome recognition to start translation.
      (6 votes)
  • blobby green style avatar for user maria
    pYrimidine has Y in it so does cYtosine and thYmine
    (4 votes)
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  • leafers ultimate style avatar for user Hamzah
    I have a question about denaturation. Is it something that is specific only to the breaking of DNA? Because in my biology lecture, the professor said that denaturation is when proteins change their structure. They are still the same because both involve breaking down, since proteins must break down to change structure, right?
    (2 votes)
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  • piceratops seedling style avatar for user Rain
    at about 1:71 isn't genetic spelled with a G instead of J? just asking if she was wrong.
    (2 votes)
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  • piceratops ultimate style avatar for user Shreya Rao
    So, one way of denaturing DNA is raising the temperature. What temperatures are we talking about here? How high would the temperature have to be?
    (2 votes)
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  • mr pink red style avatar for user PROSPER NASUWA
    When you Donate Blood to a person does that blood mix with the other person's blood?If it does, does it change it's structure to another DNA ID/Structure or is it going to stay the same?
    (1 vote)
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    • duskpin ultimate style avatar for user Blittie
      There is an interesting write up at this site answering your question: http://www.straightdope.com/columns/read/1418/does-a-blood-donation-mess-up-dna-evidence
      The summary of the article says that in blood transfusions, the blood received would be red blood cells: the donated sample would be called packed red blood. These contain no nucleus and thus have no DNA. In bone marrow transfusion however, the recipient will be making another person's blood and their DNA. So let's pretend the recipient commits a crime and has left blood behind. Does another person get blamed? Luckily, police do detective work that would take samples from more than just blood (like a witness' statement) - BUT - there is a way to detect someone who's received a transfusion - their enzymes (and I am sure the suspect would have special needs that would prompt the police to pull the doctor's records).
      (2 votes)
  • winston baby style avatar for user AJ
    Where's the part 2 of this video? I can't find it on the list.
    (1 vote)
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  • marcimus pink style avatar for user alwayswantingmore56
    How do I number the carbons in the DNA bases?
    (1 vote)
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Video transcript

- [Voiceover] If you were to take a look at a chromosome you would see see that it is made up of this very densely packed (mumbling) known as chromatin. And then if you were to further break down chromatin you would see that it's made up of tremendous amount of DNA wrapped around these proteins known as histones. And DNA stores our genetic information. We get it from our parents and we pass it on to our children and DNA basically determines the identity of all living organisms. And just some interesting facts about DNA. If you were to take the DNA that was contained in one human cell and stretch it out, it would measure about two meters or approximately six feel long. So, that is a lot of DNA to pack into a cell that's relatively so tiny. And how's that done? Well, with the help of those proteins I mentioned histones, they help to wrap DNA in a very tightly coiled and very dense fashion. Just another interesting fact: If you were to take all the DNA found in one human's body and line it up together it would measure, brace yourself for a very large number, it would measure one hundred trillion meters. That is a huge number. In fact, something that long can go around the equator of the Earth two and a half million times. So, we hold in our cells a tremendous, tremendous amount of DNA. But anyway, let's talk about the structure of this super, super important molecule that basically determines the identity of all living organisms. So, DNA's made up of three components. The first is a sugar known as deoxyribose. And it's deoxyribose because there is a sugar Ribose that has an oxygen right over here but deoxyribose doesn't have that oxygen. So, this molecule's deoxyribose and the carbons in deoxyribose are labeled. This carbon is labeled one prime, prime's first of that little apostrophe after the number. Two prime, three prime. This carbon is four prime and this carbon is five prime. And in case you're wondering why we need those primes, like, why can't we just leave all the carbons? carbon one, two, three, four, five. So, the answer to that question is that we're trying to differentiate between the carbons in this molecule. I'll explain to you in a minute what this molecule is. But, we're trying to differentiate between the carbons in this molecule and the carbons in the deoxyribose. So, for some reason, the carbons in this molecule took precedence and the carbons there are labeled one, two, three, four, five, etc. And so the carbons in deoxyribose are labeled one prime, two prime, three prime, etc. But anyway, that takes care of deoxyribose and then the next molecule in DNA is a nitrogen base. And the nitrogen base you're looking at here's actually adenine. We've heard of the molecule ATP, adenosine triphosphate, and that also has adenine in it. But anyway, there are actually four different nitrogen bases that you can find in DNA. So, I'm gonna pause for a second from what we're looking at and we're gonna take a look at those four nitrogen bases. This one here is adenine. That's the base that we just saw a moment ago. And then right next to it looking very similar is another nitrogen base guanine. And you can see that adenine and guanine are both double ring structures. On the left you can see they have a ring with six sides to it, and then attached on the right they have a ring with five sides to it. And, well, these are all called nitrogen bases 'cause they have couple nitrogens in them. And adenine and guanine are known as purines. So, the double ring bases are known as purines and I always have this hint to help me remember. So, it's really an exstrinsic hint because it has nothing to do with the material but it always helped me. So, when something is pure it glows, so purines always glow. That was my hint and then I would always remember that A stands for adenine and G always stands for guanine. So, if it helps you then use that. Then we have these other two bases. This one here is thymine. And then right next to it we have something that also looks similar to it, cytosine. And you can see thymine and cytosine are single ring structures. They only have one ring with six sides and they're known as pyrimidines. So, again, the purines are adenine and guanine and the pyrimidines are thymine and cytosine. And the purines and pyrimidines will always pair up with each other in this fashion. Adenine always pairs up with thymine and guanine always pairs up with cytosine, unless, of course, there's a problem. And I wanna just, let's just take a look at how these molecules pair up with each other. So, let's look at this diagram. So, the bonds that hold the nitrogen bases together are hydrogen bonds. So, it's hydrogen bonding that puts them together and let's just remind ourselves, a hydrogen bonding takes place in molecules that have a hydrogen attached to one of three very electronegative atoms: fluorine, or oxygen, or nitrogen. Let me remind you, electronegative means that they like to hog electrons. They pull electrons towards themselves. And what's going to happen in molecules like this is that since fluorine, or oxygen, or nitrogen hog electrons they are going to get a slightly, or maybe more than slightly, negative charge which leaves the hydrogens kind of bereft of electron density and gives them a positive charge. And then the molecules will orient themselves in a way where the positive and negative sides are attracted and attached to each other. So, let's actually take a look at what I just explains in the molecules. So, let's look at thymine and adenine. So, we have this oxygen over here which is going to be somewhat negative because it's pulling electrons away from that carbon and for in this double bond, and then these hydrogens are going to be somewhat positive because the nitrogen near them is pulling electrons away. And so they form this hydrogen bond right over here. Then we have another hydrogen bond between this positive hydrogen. Remember, it's positive because the nitrogen here is very electronegative and hogs all the electrons. And then we have this negative nitrogen because it hogs electrons from the carbons around it. So, between thymine and adenine, we're going to have two hydrogen bonds. But if you look at cytosine and guanine, there're actually three hydrogen bonds between them. So, we can see that cytosine and guanine are attached to each other a little bit more strongly than thymine and adenine and well, what would the implications of this be? So, what do we have? Two pairs of DNA. We're gonna soon see DNAs at double stranded molecule where the nitrogen bases pair up with each other, something like this. And I'm gonna label this DNA set A and this I'll label B. And let's say I tell you that in A we have a very high number of As and Ts, so, let's say most of these are As and Ts, so, I'm just gonna, I don't know, put an A here and put a, well, let's make that a little bit clearer. So, an A and then there's gonna be a T here, and let's say that most of this DNA looks like that. And let's say that B has a very, very high number of Cs and Gs. So, here's a C and here's a G, and let's say that most of the DNA looks like that. So, B has a lot of Cs and Gs. So, which DNA do you think it's gonna be harder to break? And by break, I mean basically break the bonds between the nitrogen bases just like that and make two separate strand, and that's actually called denaturization. So, to denature DNA means to kind of split it down the middle, break the nitrogen base bonds, and have two strands instead of one. So, again, which of these DNAs do you think it's going to be harder to denature, A or B? Well, we just explained that between Cs and Gs, between cytosines and guanines, there are three hydrogen bonds. So, it would be harder to break down B because it has more Cs and Gs. And so, one way to denature DNA is to raise the temperature. That's one way to break down DNA. So, breaking down DNA B is going to take a higher temperature than breaking down DNA A. That's just one example of why this fact would matter. This fact thymine and adenine have two hydrogen bonds and cytosine and guanine have three. Anyway, now that we've discussed the nitrogen bases that make up DNA let's go back to actually putting our DNA together and the various components in it. So, again, we said the first component in DNA deoxyribose. The second thing we discussed just now were the nitrogens bases and now the third component in DNA is going to be a phosphate group. And actually, what I drew was a triphosphate. It's three phosphates together and I drew it as a triphosphate because we start off with a triphosphate but eventually two of the phosphates get lopped off and we're gonna be left with only one phosphate group. So, we're gonna pause out and in part two of this topic we're gonna pick up on this and see how we put together all of these components to make the DNA that we have in our cells.