DNA IV base orientation


the strands are backward, relative to each other “DNA is antiparallel” refers to the ribose phosphate chain
it really doesn’t have anything to do with the bases let’s turn our attention to the bases adenine is a good example adenine, the molecule is flat, the molecule of adenine, the base,
has no symmetry, whatsoever left to right,,,,, top to bottom ,,,,front to back
there is no symmetry to it whatsoever adenine, of course, combines with two hydrogen bonds with thymine and thymine has no symmetry…. adenine has no symmetry the base pair, adenine/thymine have no symmetry whatsoever they are always combined in the same way. Similarly guanine combines with cytosine this time with three base pairs (hydrogen bonds) the guanine/cytosine base pair….
there is not a variation and how it can happen the cytosine cannot be upside down it’s always right side up
it all was makes the same base pair so,, if we look at DNA as a spiral staircase the stair steps are (adenine thymine) and (guanine and cytosine) the stair steps are not….there are not variations
in the structure of the stair steps let’s turn our attention to this guy this is a common drawing of DNA. I’ve looked at many many
of these and they are all the same Which is to say that none of them are wrong
or they are very consistent in the way they are drawn say, we take the adenine…let’s have the adenine as the codon so the adenine is the codon and it fits right here and then, of course, thymine is the anticodon. let’s say we want to have the adenine as the anticodon
which of course, puts the thymine as the codon so….the strands are antiparallel so, we turn this around and we find an adenine here
and put the sugar (ribose) on so it matches…so the stands are antiparallel.. but notice that the adenine does not fit The adenine has to be turned back over in order to fit. So….let’s go back to these guys we got (adenine thymine) (guanine and cytosine) these guys …..each one of them let’s start with (adenine thymine) (adenine thymine) has …….. let’s make adenine the codon we have two possibilities
we have this one and then you know I have drawn it
so this must be the top no , this is not the top necessarily
this is just the way I have drawn it it can also be like this okay and then of course if the ……If adenine is the codon the thymine is the anticodon let’s make thymine the codon and adenine the anticodon… okay what are the possibilities this time we have thymine as the codon and adenine as the anticodon but there is another possibility and that is that this could be turned over this way the top to bottom business is something
that we kind of makeup as human beings it isn’t really ….there isn’t a lot of reality to that so this looks like it’s upside down but it’s relatively its upside down relative to how I have drawn it it’s really not …. what’s upside down and what’s not upside down okay let’s look at the guanine and cytosine in the same way we have guanine is the codon
…so there is two possibilities it can go like this… guanine is the codon
or it can be upside down guanine can be the codon and cytosine can be the anticodon and then of course the last one is cytosine and then guanine is the anticodon, but it can be turned over so every base has four possible orientations which are too many….. which is to many orientations
we really only want two let’s go back to this thing okay we have guanine… let’s look at guanine as the anticodon so guanine is the anticodon, notice how it fits if we turn this over …make the ribose ….make it the anti-parallel look at the ribose this is guanine
notice the three hydrogen bonds the guanine doesn’t fit if we turn it over it does fit and then finally if we take this one …..is a thymine this is an adenine/thymine so we have the adenine is the codon and the thymine is the anticodon okay let’s turn it over and find ..
..this is a thymine… (adenine thiamine) … …if we put this guy on here it doesn’t work unless
the base is turned over so the conclusion seems to be that with thymine, for example, as the codon
the base pair has one orientation with adenine as the codon the base pair (stairstep) is turned over to repeat with the other base pair if cytosine is the codon with guanine as the codon
the base pair (stairstep) is turned over. I have here representations of the base pairs. this is (cytosine guanine) this is (adenine thiamine) these are representations of the base pairs they have a front and back which is, of course, the same as a real… a real base pair as the top and bottom
which are different these have a top and bottom which are different we are wondering if, with adenine as the codon
the base is not upside down if thymine is the codon so, let’s kind of just move forward with this as an experiment we pick one let’s use the codon on this side let’s put adenine as the codon and put the black stripe up okay we have thymine as the codon but were thinking that it’s upside down so, let’s go ahead and turn it over…. so adenine is black stripe up thymine is black stripe down. okay, we have to cytosine… let’s just put the cytosine on we put the cytosine on okay we have an adenine…adenine we think is black stripe up so let’s go ahead and put the black strip up for adenine okay we have a guanine ….well if cytosine is normal
then guanine is going to be black stripe up so let’s go ahead and put a guanine on okay we have another guanine ….cytosine is white stripe up so let’s put guanine on okay so what do we have here let’s go ahead and take this guy off. and take a look at it we have ….like a representation of the stacked base pairs let’s say we want to look down this side. we have four possibilities we have red on the left and red on the right and we have green on the left and green on the right the cytosine guanine base pair ….it’s always the same edge facing up they’re oriented differently like the symmetry is different and then the other side is…… we have these are all black so it’s a little harder to see but again there are four possibilities there is a dot left and right and a stripe left and right for the (cytosine guanine) base pair and the (adenine/thymine) base pair there is two orientations for each one the dogma of genetics is, of course, the RNA is transcribed against the anticodon of the DNA so that, against the anticodon, the RNA picks up the codon which is kind of the idea and then the RNA goes out into the cytoplasm
and becomes translated into protein so the codon of the DNA
describes the amino acid sequence in the protein but, as important a question is: “Where does the RNA start and where does the RNA stop??” what determines where the RNA does it’s thing there are whole families of proteins that spend all their time in the major grove they are inducers and transcription factors and repressors and there are bunches and bunches of them the transcription factors look at the edges of the bases
and determine what’s going on based upon feeling the edges of the bases and the major grove looks at one set and
the minor groove looks at a completely different set the major grove is bigger that the minor groove and it would make sense that proteins which hang out in the major grove, which are most of these compounds, don’t go into the minor groove …… ……and that’s it ……and that’s it

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