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<!DOCTYPE TEI.2 SYSTEM "base.dtd">





<publicationStmt><distributor>BASE and Oxford Text Archive</distributor>


<availability><p>The British Academic Spoken English (BASE) corpus was developed at the

Universities of Warwick and Reading, under the directorship of Hilary Nesi

(Centre for English Language Teacher Education, Warwick) and Paul Thompson

(Department of Applied Linguistics, Reading), with funding from BALEAP,

EURALEX, the British Academy and the Arts and Humanities Research Board. The

original recordings are held at the Universities of Warwick and Reading, and

at the Oxford Text Archive and may be consulted by bona fide researchers

upon written application to any of the holding bodies.

The BASE corpus is freely available to researchers who agree to the

following conditions:</p>

<p>1. The recordings and transcriptions should not be modified in any


<p>2. The recordings and transcriptions should be used for research purposes

only; they should not be reproduced in teaching materials</p>

<p>3. The recordings and transcriptions should not be reproduced in full for

a wider audience/readership, although researchers are free to quote short

passages of text (up to 200 running words from any given speech event)</p>

<p>4. The corpus developers should be informed of all presentations or

publications arising from analysis of the corpus</p><p>

Researchers should acknowledge their use of the corpus using the following

form of words:

The recordings and transcriptions used in this study come from the British

Academic Spoken English (BASE) corpus, which was developed at the

Universities of Warwick and Reading under the directorship of Hilary Nesi

(Warwick) and Paul Thompson (Reading). Corpus development was assisted by

funding from the Universities of Warwick and Reading, BALEAP, EURALEX, the

British Academy and the Arts and Humanities Research Board. </p></availability>




<recording dur="00:53:53" n="7344">


<respStmt><name>BASE team</name>



<langUsage><language id="en">English</language>



<person id="nm0238" role="main speaker" n="n" sex="m"><p>nm0238, main speaker, non-student, male</p></person>

<personGrp id="ss" role="audience" size="l"><p>ss, audience, large group </p></personGrp>

<personGrp id="sl" role="all" size="l"><p>sl, all, large group</p></personGrp>

<personGrp role="speakers" size="3"><p>number of speakers: 3</p></personGrp>





<item n="speechevent">Lecture</item>

<item n="acaddept">Animal and Microbial Sciences</item>

<item n="acaddiv">ls</item>

<item n="partlevel">UG1</item>

<item n="module">Genetics and molecular biology</item>




<u who="nm0238"> okay good morning <trunc>everyb</trunc> <pause dur="0.3"/> good <trunc>af</trunc> <gap reason="inaudible" extent="1 word"/> <pause dur="0.8"/> it's Friday i don't even know whether it's morning or afternoon <pause dur="0.5"/> good afternoon everyone <pause dur="0.9"/> # i hope you're all <pause dur="0.6"/> comfortable and have switched your mobiles off <pause dur="1.3"/> so that we have a nice quiet time apart from me <pause dur="1.1"/> # <pause dur="0.6"/> first of all a reminder <pause dur="1.0"/> about the practical sessions this afternoon and of course i'll put this up again later <pause dur="0.9"/> # <pause dur="2.0"/> group D are doing practical three in A-M-S-G-eight <pause dur="1.3"/> group A are over in Plant Sciences lab B doing <pause dur="0.8"/> the # <pause dur="0.2"/> mitosis practical i think <pause dur="1.8"/> the miosis practical and group C are doing the wash up practical one with me <pause dur="0.5"/> in G-four <pause dur="5.3"/> we're also # <pause dur="0.2"/> we also welcome to this session <pause dur="1.0"/> a member of the # Centre for Applied Language Studies staff <pause dur="0.8"/> who thinks # that this <pause dur="1.2"/> lecture may be worth recording <pause dur="1.5"/> well there we go <pause dur="4.6"/><kinesic desc="puts on transparency" iterated="n"/> my topic <pause dur="0.3"/> for the first session this afternoon <pause dur="0.8"/> is D-N-A and information <pause dur="2.1"/> we've spent a long time now <pause dur="0.4"/> # talking about genetics <pause dur="1.5"/> about <pause dur="0.7"/> <trunc>m</trunc> <pause dur="0.2"/> genetics at the level of the <pause dur="0.4"/> individual <pause dur="0.3"/> at the level of the phenotype <pause dur="0.7"/> at the

level of the population <pause dur="0.2"/> last week <pause dur="1.3"/><vocal desc="clears throat" iterated="n"/><pause dur="0.2"/> and at the level of the gene <pause dur="0.8"/> undefined idealistic gene <pause dur="0.5"/> Mendel's gene <pause dur="2.2"/> which we've identified so far with a locus on a chromosome <pause dur="1.8"/> but always at the back of our minds has been the fact that we all know that we live in the post-D-N-A age <pause dur="1.0"/> and there is another way of explaing genetic behaviour <pause dur="0.5"/> and that is to explain it at the molecular level <pause dur="0.7"/> to explain it in terms of this molecule <pause dur="0.5"/> deoxyribonucleic acid <pause dur="1.5"/> D-N-A <pause dur="2.1"/> and at about the same time that we discovered that D-N-A was the genetic <trunc>informa</trunc> the genetic # material <pause dur="1.4"/> we also <pause dur="0.6"/> were powerfully influenced by a theory <pause dur="0.5"/> that said genetic material must consist of information <pause dur="0.8"/> this was <pause dur="0.4"/> a theory <pause dur="0.8"/> which was based on <pause dur="0.8"/> early computer theory <pause dur="0.8"/> # <pause dur="0.6"/> but was much supported by <pause dur="1.3"/> the famous physicist Erwin Shrödinger <pause dur="0.9"/> who during the last war <pause dur="0.4"/> lived understandably away from Germany in Dublin <pause dur="0.5"/> and he gave a very powerful <pause dur="0.2"/> series of lectures in Dublin called What is Life <pause dur="0.8"/> in which he propounded the

view <pause dur="0.7"/> that <pause dur="0.3"/> at the bottom of life was genetics <pause dur="0.4"/> and at the bottom of genetics had to be some sort of information <pause dur="0.5"/> so we'll look at that information <pause dur="0.3"/> paradigm or model <pause dur="0.6"/> of # <pause dur="0.6"/> genetics alongside <pause dur="0.5"/> # <pause dur="0.3"/> information about D-N-A <pause dur="1.3"/> now i know that there are some of you <pause dur="0.6"/> who will have been talking about D-N-A <pause dur="0.5"/> for many years now and will be <pause dur="0.4"/> if <trunc>an</trunc> if <trunc>y</trunc> if it's possible to be <pause dur="0.6"/> and since i'm a D-N-A biochemist i don't think it's possible to be <pause dur="0.8"/> # may actually be bored with it <pause dur="0.7"/> well we'll try and <pause dur="0.3"/> # liven it up as much as we can <pause dur="0.2"/> when we talk <pause dur="2.6"/> the substance of this lecture <pause dur="1.0"/> has three parts <pause dur="1.0"/> # we're going to remind ourselves what the evidence is <pause dur="0.4"/> for D-N-A as the genetic material <pause dur="0.9"/> then we're going to look at nucleic acids as molecules <pause dur="1.1"/> and finally we're going to look at the functionality of D-N-A <pause dur="1.0"/> how this model of D-N-A as information maps onto biochemical mechanisms <pause dur="1.4"/> and in my second talk this afternoon we'll move on to talk a bit more about that <pause dur="3.6"/> so the evidence first of all then for D-N-A

as the genetic material <pause dur="3.3"/><kinesic desc="changes slide" iterated="n"/> and there are two <pause dur="2.3"/> two canonical experiments <pause dur="0.9"/> # <pause dur="1.1"/> which <pause dur="0.5"/> are described <pause dur="0.2"/> in <pause dur="1.1"/> chapter sixteen of Campbell <pause dur="0.9"/> # and one of which we have already talked about so i will talk about the second today <pause dur="1.1"/> the first one is the transformation experiment <pause dur="0.8"/> which we talked about when we were talking about transformation <pause dur="0.5"/> in our consideration of bacterial genetics <pause dur="0.6"/> remember transformation is when <pause dur="0.3"/> an external D-N-A source <pause dur="0.6"/> # <pause dur="0.3"/> is added to a bacterium the bacterium takes up the D-N-A <pause dur="0.4"/> and changes <pause dur="0.2"/> its # <pause dur="0.7"/> phenotype <pause dur="0.3"/> in response to that new genetic information <pause dur="1.2"/> and you'll remember <pause dur="0.6"/> that this was originally <pause dur="0.3"/> studied by the <pause dur="0.2"/> English bacteriologist Griffith <pause dur="0.9"/> when he looked at rough and smooth pneumococci <pause dur="0.5"/> bacteria that caused <pause dur="0.3"/> lung disease <pause dur="0.5"/> and killed <pause dur="0.2"/> mice <pause dur="1.4"/> if they were smooth but not if they were rough <pause dur="0.8"/> and then he showed that an extract of D-N-A from the smooth bacteria <pause dur="0.4"/> could transform the rough bacteria <pause dur="0.3"/> to make those equally pathogenic <pause dur="1.3"/> now of course at that point you remember <pause dur="0.3"/> he didn't

know anything about what it was <pause dur="0.4"/> that was the transforming agent as he called it <pause dur="1.1"/> # but <pause dur="0.3"/> subsequently <pause dur="0.4"/> three researchers <pause dur="0.2"/> in Baltimore <pause dur="0.9"/> Avery MacLeod and McCarty <pause dur="0.4"/> went through a series of experiments <pause dur="0.3"/> where they digested <pause dur="0.6"/> that <pause dur="0.4"/> # preparation of transforming agent <pause dur="0.5"/> with different enzymes <pause dur="0.7"/> so they <pause dur="0.2"/> digested it with <pause dur="0.2"/> enzymes which <pause dur="0.7"/> # broke down protein <pause dur="0.4"/> which broke down R-N-A <pause dur="0.3"/> which broke down sugars <pause dur="0.3"/> which broke down D-N-A <pause dur="0.5"/> and they discovered that the only set of enzymes which killed <pause dur="0.7"/> the ability of the extract to transform <pause dur="0.4"/> were the <pause dur="0.5"/> D-N-A <pause dur="0.2"/> breaking down enzymea D-N-A-ases <pause dur="0.6"/> nucleases <pause dur="1.2"/> and so they came to the conclusion that D-N-A <pause dur="0.3"/> must be <pause dur="0.4"/> the transforming agent <pause dur="0.5"/> and hence <pause dur="0.3"/> what it was <pause dur="0.7"/> that was in <pause dur="0.9"/> the smooth bacteria <pause dur="0.3"/> which <pause dur="0.5"/> when donated to the rough bacteria made them pathogenic <pause dur="2.4"/> the second <pause dur="1.0"/> experiment <pause dur="0.5"/> is known <pause dur="0.3"/> throughout biochemistry as the blender experiment <pause dur="1.4"/> because <pause dur="0.2"/> # <pause dur="0.2"/> a material part in the experiment is taken by an ordinary kitchen blender <pause dur="2.4"/> and that is described <pause dur="1.1"/><kinesic desc="changes transparency" iterated="y" dur="2"/> on this overhead which you have a

copy <pause dur="0.4"/> of <pause dur="1.3"/> in your handout <pause dur="1.2"/> it's more properly known at the Hershey-Chase experiment <pause dur="1.3"/> not for those of you who come from the other side of the water because it has anything to do with chocolate bars <pause dur="0.5"/> but because <pause dur="0.9"/> there was a man called Hershey and a man called Chase <pause dur="0.3"/> in fact a woman called Chase <pause dur="0.6"/> # who did this experiment <pause dur="1.6"/> and this brings us back <pause dur="0.5"/> again <pause dur="0.5"/> to our consideration of bacterial genetics because it involves one of those organisms <pause dur="0.4"/> we talked about in bacterial genetics <pause dur="0.3"/> that is the bacteriophage <pause dur="1.1"/> and you'll remember this picture <pause dur="0.5"/> of a bacteriophage looking rather like <pause dur="0.6"/> a lunar module <pause dur="1.5"/> here attaching to a host bacterium <pause dur="1.9"/> well what Hershey and Chase tried to do <pause dur="0.5"/> was to show what it was <pause dur="0.9"/> that a phage <pause dur="0.3"/> injected into <pause dur="0.4"/> the host bacterium <pause dur="0.6"/> which enabled that host bacterium to become then <pause dur="0.4"/> a machine <pause dur="0.3"/> for constructing new phage <pause dur="1.8"/> and they did that using what was at that time very new technology <pause dur="1.6"/> they <pause dur="0.2"/> # <pause dur="0.2"/> radioactively labelled <pause dur="0.3"/> their phage <pause dur="1.1"/> and they used <pause dur="0.7"/> two radioactive labels <pause dur="0.9"/> thirty-five-sulphur <pause dur="0.7"/>

and <pause dur="0.4"/> thirty-two-<pause dur="0.2"/>phosphorus <pause dur="1.1"/> so the <pause dur="0.2"/> the upper line of this <pause dur="0.3"/> describes what happens <pause dur="0.4"/> # with thirty-five-sulphur <pause dur="0.7"/> and the bottom line <pause dur="0.4"/> describes what happens with thirty-two-phosphorus <pause dur="0.8"/> the reason they used the two labels <pause dur="0.6"/> is <pause dur="0.5"/> that <pause dur="0.4"/> there is <pause dur="0.2"/> quite a lot of sulphur <pause dur="0.5"/> in <pause dur="0.9"/> proteins <pause dur="0.3"/> coming from the amino acids methionine and cysteine <pause dur="1.2"/> and very little phosphate <pause dur="1.3"/> whereas there is a great deal of phosphate <pause dur="0.6"/> in nucleic acids <pause dur="0.3"/> and no sulphur <pause dur="1.4"/> so using these two labels <pause dur="0.6"/> the thirty-five-S showing what the protein is doing <pause dur="0.5"/> and the thirty-two-P <pause dur="0.3"/> showing what the <pause dur="0.3"/> nucleic acid is doing <pause dur="0.4"/> they hoped to be able to show what it was <pause dur="0.3"/> that got into the bacterium <pause dur="0.5"/> and caused <pause dur="0.4"/> the # <pause dur="2.2"/> caused the # <pause dur="1.0"/> genetic changes in the bacterium <pause dur="1.2"/> so <pause dur="0.8"/> in both experiments what you do is to take your radioactively labelled phages <pause dur="0.6"/> in a a flask you infect <pause dur="0.2"/> some E-coli bacteria with those radioactively labelled phages <pause dur="0.4"/> and you allow them to attach <pause dur="1.6"/> and even after they've injected their genetic information into the host cell <pause dur="0.4"/> they will

remain attached so we have to detach them <pause dur="0.6"/> and the way we do that is to use the sheer forces generated by an ordinary kitchen blender <pause dur="0.8"/> so you put your mixture <pause dur="0.2"/> into <pause dur="0.3"/> the blender <pause dur="0.7"/> and you whirl it around a bit <pause dur="0.9"/> and then you use a centrifuge <pause dur="0.5"/> to separate <pause dur="0.2"/> the supernatant <pause dur="0.4"/> which contains the phage particles that have broken off from the outside of the bacteria <pause dur="0.5"/> and the pellet <pause dur="0.2"/> which contains the bacteria <pause dur="1.6"/> and when you do that <pause dur="0.6"/> and you do it with thirty-five-sulphur <pause dur="0.8"/> then all the <pause dur="0.5"/> radioactivity remains in the supernatant <pause dur="0.7"/> but when you do it with radioactive phosphorus <pause dur="0.5"/> all the radioactivity <pause dur="0.5"/> is in the pellet <pause dur="0.8"/> so you know that it's the phosphorus <pause dur="0.4"/> from the bacteria from the phage that's entered the bacteria <pause dur="0.3"/> and not the thirty-five-<pause dur="0.4"/>S <pause dur="0.5"/> and so we conclude <pause dur="0.3"/> that it's the nucleic acids in the phage <pause dur="0.4"/> that are carrying the genetic information <pause dur="0.2"/> and not the protein <pause dur="1.3"/> okay <pause dur="0.4"/> another very <pause dur="0.2"/> simple experiment it looks <trunc>t</trunc> almost trivially simple to us now <pause dur="0.6"/> # <pause dur="0.5"/> but it was very instrumental <pause dur="0.5"/> in showing <pause dur="0.5"/> that D-N-A

was the genetic information so now we were able to show <pause dur="0.6"/> that in bacterial transformation <pause dur="0.2"/> and in phage infection <pause dur="0.7"/> the genetic information that was being transferred <pause dur="0.7"/> was <pause dur="0.3"/> a nucleic acid <pause dur="0.4"/> and in particular <pause dur="0.2"/> D-N-A <pause dur="5.2"/><kinesic desc="changes slide" iterated="n"/> so we now know that D-N-A is the genetic material <pause dur="0.7"/> what sort of stuff <pause dur="0.5"/> is D-N-A <pause dur="3.2"/> and in general what sort of <pause dur="0.4"/> stuff <pause dur="0.3"/> are nucleic acids <pause dur="2.4"/> well nucleic acids <pause dur="0.5"/> as you all know are polymers <pause dur="1.5"/> and in the case of D-N-A strikingly long <pause dur="0.2"/> polymers <pause dur="0.5"/> polymers being <pause dur="0.2"/> chemicals which are constructed from repeating simpler units <pause dur="4.9"/> the base unit <pause dur="0.7"/> of a nucleic acid is what we call a polynucleotide <pause dur="1.8"/> okay and so <pause dur="0.3"/> this is an appropriate point to remind ourselves what a nucleotide is <pause dur="11.1"/><kinesic desc="changes slide" iterated="n"/>

and basically a nucleotide <pause dur="1.3"/> is a combination of three things <pause dur="0.5"/><kinesic desc="writes on transparency" iterated="y" dur="4"/> a base <pause dur="0.7"/> a sugar <pause dur="0.6"/> and a phosphate <pause dur="0.9"/> and for those of you who like like like their chemistry really simple and i'm sure that applies to a lot of you <pause dur="1.3"/> we can think <pause dur="0.2"/> of a nucleotide <pause dur="0.2"/> as being constructed in a very simple way <pause dur="1.2"/> with a base <pause dur="0.9"/> here <pause dur="0.8"/> bonded <pause dur="0.8"/> by a single bond <pause dur="0.7"/> to a sugar <pause dur="5.2"/> and that sugar being again bonded <pause dur="0.6"/> by a single bond <pause dur="0.2"/> to a phosphorus <pause dur="1.9"/> okay <pause dur="1.2"/> now this bond here <pause dur="0.2"/> is an oxygen <trunc>phos</trunc> <pause dur="0.2"/> # carbon-oxygen-phosphorus bond <pause dur="0.6"/> this bond here <pause dur="0.4"/> is a carbon-nitrogen bond <pause dur="0.5"/> but # <pause dur="0.3"/> that's for the chemists to worry about most of us <pause dur="0.8"/> not too worried about that <pause dur="2.7"/> but those of us who <pause dur="0.6"/> <trunc>w</trunc> <pause dur="0.7"/> and all of you should have at least some familiarity with what those chemicals look like <pause dur="0.4"/> whether you like it or not <pause dur="6.8"/><kinesic desc="changes transparency" iterated="y" dur="13"/> we'll look at <pause dur="0.8"/> a slightly more complicated version <pause dur="0.3"/> of what those chemicals look like <pause dur="5.1"/> okay so <pause dur="0.4"/> our bases <pause dur="1.7"/> right <pause dur="0.4"/> can be any of <pause dur="0.9"/> in the case of D-N-A <pause dur="0.5"/> four <pause dur="0.2"/> different bases <pause dur="0.5"/>

adenine <pause dur="0.2"/> guanine cytosine <pause dur="0.3"/> and <pause dur="0.2"/> thymine <pause dur="2.7"/> and in the case of R-N-A <pause dur="0.5"/> any of the four bases adenine guanine cytosine or uracil <pause dur="4.3"/> the difference between those <pause dur="0.4"/> different bases <pause dur="0.8"/> what we have there is a picture of thymine and uracil <pause dur="2.1"/><kinesic desc="changes transparency" iterated="y" dur="8"/> but adenine <pause dur="2.5"/> is a typical base <pause dur="0.7"/> of the other kind so let's just draw <pause dur="1.2"/> the two kinds of D-N-A bases you've seen thymine which looks like this <pause dur="12.4"/><kinesic desc="writes on transparency" iterated="y" dur="26"/> okay that's thymine <pause dur="1.5"/> and thymine is what we call a <trunc>pur</trunc> <pause dur="0.2"/> a pyrimidine base <pause dur="3.6"/> and it just has a single <pause dur="1.4"/> aromatic ring <pause dur="1.5"/> okay <pause dur="0.2"/> and that aromatic ring contains two nitrogens <pause dur="0.9"/> the difference between thymine <pause dur="0.4"/> cytosine and uracil <pause dur="0.3"/> which are the three pyrimide bases <pause dur="0.4"/> lies in what substituents we have <pause dur="0.6"/> in the case of thymine and uracil it's two oxygens <pause dur="0.5"/> in the case <pause dur="0.2"/> of # cytosine it's an oxygen and a nitrogen <pause dur="2.2"/> if we look at the pyrimidine bases they're slightly different and slightly more complicated <pause dur="17.6"/><kinesic desc="writes on transparency" iterated="y" dur="30"/> just try and draw the bonds right <pause dur="0.7"/> okay that's adenine <pause dur="3.5"/> which is the simplest of these more complex bases which are

called purines <pause dur="2.2"/> okay <pause dur="0.3"/> so there are two types of bases purines and pyrimidines <pause dur="2.1"/> one is a single ring <pause dur="0.7"/> and the slightly longer name <pause dur="0.4"/> smaller structure longer name <pause dur="0.5"/> and the other one has a double ring <pause dur="0.5"/> and a shorter name <pause dur="1.2"/> okay as well as thymine in this class we have <pause dur="0.6"/> cytosine <pause dur="1.0"/> and uracil <pause dur="1.3"/> and as well as adenine in this class we have guanine <pause dur="4.1"/> and the differences as i said are in the number of substituents in the ring <pause dur="0.5"/> if you want to know more <pause dur="0.2"/> about that <pause dur="0.3"/> chapter sixteen of Campbell <pause dur="0.4"/> is where you look <pause dur="1.9"/> so those are the bases <pause dur="1.4"/> those bases are linked <pause dur="0.2"/> to sugars <pause dur="2.0"/> deoxyribose <pause dur="0.2"/> in the case of D-N-A <pause dur="0.3"/> ribose <pause dur="0.4"/> in the case of R-N-A <pause dur="0.5"/> both of them sugars containing <pause dur="0.3"/> five carbons <pause dur="0.6"/> one two three four five <pause dur="0.3"/> one two three four five <pause dur="0.3"/> arranged in a five-membered ring <pause dur="0.5"/> with one of their oxygens <pause dur="1.1"/> and then this is linked <pause dur="0.9"/> to a phosphate group <pause dur="0.6"/> and that phosphate group is linked through this carbon here <pause dur="0.5"/> the so-called five-prime carbon <pause dur="3.3"/> and as you see <pause dur="0.5"/> these nucleotides are linked together in a strand <pause dur="0.2"/> up to a

polynucleotide <pause dur="0.5"/> by bonds <pause dur="0.4"/> between <pause dur="0.7"/> the phosphate which is on the five-prime <pause dur="0.5"/> on the five-prime carbon of this <pause dur="1.1"/> sugar <pause dur="0.6"/> is linked <pause dur="0.4"/> to the three-prime carbon <pause dur="0.5"/> of the next sugar <pause dur="0.5"/> so what we have is a chain going sugar phosphate sugar phosphate sugar phosphate sugar phosphate sugar phosphate <pause dur="0.4"/> and off it we have the bases <pause dur="0.7"/> so it's like a ladder structure <pause dur="0.6"/> sugars and phosphates <pause dur="0.5"/> but with bases intervening <pause dur="1.4"/> so if we <pause dur="0.4"/> were to put that back on my simple minded diagram <pause dur="1.1"/> okay here's base sugar phosphate <pause dur="0.6"/> what i would have <pause dur="0.7"/> then <pause dur="0.2"/><kinesic desc="writes on transparency" iterated="y" dur="15"/> is this sugar here <pause dur="0.6"/> joining on to another phosphate here <pause dur="0.8"/> and then <pause dur="0.3"/> another sugar <pause dur="1.1"/> here <pause dur="0.4"/> and another base <pause dur="0.6"/> here <pause dur="1.4"/> and then this sugar <pause dur="0.3"/> again joining on <pause dur="0.9"/> to another phosphate <pause dur="1.0"/> and so on and so on <pause dur="0.9"/> phosphate sugar phosphate sugar phosphate sugar <pause dur="4.9"/> so that in very simple terms <pause dur="1.1"/> is how you make a nucleotide <pause dur="0.5"/> something about the nomenclature <pause dur="2.2"/> well we found that there are five bases adenine guanine thymine cytosine and <pause dur="0.6"/> # <pause dur="0.4"/> uracil <pause dur="1.2"/> in fact <pause dur="0.2"/> as nucleotides they all change their names just to be very

awkward <pause dur="1.6"/> and <pause dur="0.2"/> adenine changes to adenosine <pause dur="1.2"/> cytosine to cytidine <pause dur="0.5"/> guanine to guanosine <pause dur="0.8"/> and uracil and thymine <pause dur="1.0"/> well there is no no uracil changes to uridine and thymine to thymidine <pause dur="0.3"/> again this is something you don't have to take in now <pause dur="0.6"/> <trunc>perha</trunc> # any book will tell you those names <pause dur="3.9"/> and we've looked at how to build a polynucleotide we build a polynucleotide by joining these units through <pause dur="0.2"/> base # through sugar phosphate <pause dur="0.2"/> linkages <pause dur="4.4"/><kinesic desc="changes slide" iterated="n"/> we've also in talking about nucleotides <pause dur="0.4"/> discovered some of the differences <pause dur="0.3"/> between D-N-A and R-N-A <pause dur="1.0"/> we've discovered that D-N-A <pause dur="0.3"/> has thymine as one of its bases whereas <trunc>r</trunc> R-N-A has uracil <pause dur="0.3"/> that D-N-A has deoxyribose <pause dur="0.5"/> <trunc>ra</trunc> where <pause dur="0.6"/> # uracil <pause dur="0.3"/> <trunc>ha</trunc> # where <pause dur="0.3"/> R-N-A has ribose <pause dur="0.7"/> but there are one or two other <pause dur="0.5"/> structural differences that perhaps we might like to look at <pause dur="0.9"/><kinesic desc="changes slide" iterated="n"/> and one of those <pause dur="6.8"/> while we're looking at it <pause dur="5.1"/> is that D-N-A <pause dur="0.5"/> in general <pause dur="1.1"/> forms a double helix <pause dur="0.4"/> of two chains of polynucleotide <pause dur="1.3"/> and is in general <pause dur="0.2"/> a very long polymer <pause dur="0.5"/> which has a fibrous structure <pause dur="1.4"/>

whereas R-N-A <pause dur="0.7"/> is normally <pause dur="0.2"/> consist of one polynucleotide chain it is single stranded <pause dur="0.8"/> whereas D-N-A is double stranded <pause dur="0.5"/> and in general R-N-A <pause dur="0.3"/> chains tend to be <pause dur="0.2"/> short <pause dur="0.6"/> and <pause dur="0.2"/> therefore fold upon themselves <pause dur="0.3"/> to make globular molecules a bit like proteins <pause dur="0.9"/> okay so D-N-A is a double helix long and fibrous <pause dur="0.3"/> R-N-A a single stranded molecule <pause dur="0.3"/> short <pause dur="0.2"/> and globular <pause dur="2.3"/> don't know whether you've ever thought <pause dur="0.4"/> how big <pause dur="0.4"/> D-N-A might be <pause dur="0.3"/> it's a long molecule <pause dur="1.3"/> # <pause dur="1.1"/> my my <pause dur="0.4"/> favourite model for it is a <pause dur="0.6"/> a piece of <pause dur="0.8"/><kinesic desc="holds up reel of cotton thread" iterated="n"/> ordinary sewing cotton <pause dur="0.4"/> which is a roughly one in a hundred-thousand scale model <pause dur="0.8"/> okay it's one in it's a hundred-thousand times larger than a piece of D-N-A <pause dur="1.1"/> # <pause dur="0.7"/> and on this model <pause dur="1.1"/> # the amount of D-N-A in a bacterium <pause dur="1.0"/> would be a couple of hundred metres <pause dur="0.2"/> of this <pause dur="0.5"/> okay <pause dur="0.7"/> couple of hundred metres is actually <pause dur="0.3"/> more or less the contents of this # <pause dur="0.8"/> this rather large <pause dur="0.8"/> bit of cotton <pause dur="0.6"/> if you can imagine me unravelling all this of course you can see what a problem D-N-A is to keep anywhere <pause dur="0.5"/> okay <pause dur="0.7"/> such a

long molecule clearly although # one draws it conventionally as a nice little tiny circle <pause dur="0.5"/> is # <pause dur="0.2"/> somewhat complex and rather inclined to get muddled <pause dur="0.2"/> and twisted <pause dur="0.5"/> and that's a problem <pause dur="2.0"/> for a bacterium as i said about two-hundred metres of this stuff <pause dur="0.4"/> # <pause dur="0.7"/> in each cell in your body <pause dur="1.1"/> right using this model <pause dur="0.6"/> you have a hundred-and-six <pause dur="0.2"/> kilometres <pause dur="1.5"/> okay <pause dur="0.7"/> of this stuff <pause dur="0.3"/> okay <pause dur="1.0"/> it's it's actually if the real stuff <pause dur="0.3"/> okay so we scale this down a hundred-thousand times <pause dur="0.6"/> is around one-point-six metres <pause dur="1.7"/> okay <pause dur="1.2"/> one-point-six metres <pause dur="0.5"/> so it's roughly the height of a less than average man that's me <pause dur="0.4"/> # <pause dur="0.2"/> okay # roughly my height in D-N-A <pause dur="0.7"/> if you can imagine <pause dur="0.2"/> an a D-N-A molecule my height and <pause dur="0.2"/> ten-thousand <pause dur="0.3"/> hundred-thousand times thinner than that <pause dur="0.7"/> # that's how much D-N-A you've got inside every one of your cells i said a hundred-and-six kilometres didn't i <pause dur="0.4"/> it's a hundred-and-six miles <pause dur="1.2"/> to well it makes it more familiar <pause dur="0.6"/> a hundred-and-six so a hundred-and-sixty kilometres <pause dur="0.8"/> # <pause dur="0.4"/> roughly from here to Bristol <pause dur="0.5"/> so i

would have to stretch this stuff from here to Bristol <pause dur="0.3"/> to model <pause dur="0.3"/> the D-N-A inside each one of your cells <pause dur="0.9"/> so it's very long <pause dur="0.7"/> and even given <pause dur="0.5"/> that inside every one of your cells there are actually forty-some chromosomes so <trunc>th</trunc> it's not <pause dur="0.7"/> one molecule <pause dur="0.6"/> a hundred-and-six miles long <pause dur="0.6"/> it's # forty molecules adding up to a hundred-and-six miles <pause dur="0.9"/> # forty-eight molecules of course <pause dur="1.0"/> # <pause dur="0.8"/> but # that does give you some idea of scale <pause dur="1.9"/> that contains <pause dur="0.4"/> three-<pause dur="0.3"/>thousand-<pause dur="0.2"/>million <pause dur="0.9"/> nucleotides <pause dur="0.7"/> okay roughly we believe that <pause dur="0.3"/> each <pause dur="0.3"/> each D-N-A <gap reason="inaudible" extent="1 sec"/> D-N-A <pause dur="0.6"/> in one <pause dur="0.8"/> haploid amount of D-N-A <pause dur="0.2"/> in one of your cells is three-<pause dur="0.3"/>thousand-<pause dur="0.2"/>million nucleotides <pause dur="1.6"/> whereas for a our poor old friend <pause dur="0.4"/> # the # <pause dur="0.3"/> E-coli bacterium it's only some four-million <pause dur="0.5"/> a trifling amount <pause dur="3.5"/> just to go back to the molecules for a minute <pause dur="1.4"/> looking at D-N-A <pause dur="0.5"/> you know that D-N-A <pause dur="0.2"/> is a double helix <pause dur="1.4"/> okay there are some pictures of the double helix there <pause dur="5.0"/> two things about the double helix i think we need to # <pause dur="0.5"/> well at least two things we need to

talk about <pause dur="0.4"/> one of them is how the double helix is bonded together <pause dur="1.0"/> there are two sorts of bonds which hold the double helix together <pause dur="0.8"/> one of those are so-called <pause dur="0.6"/> # base pairs <pause dur="0.8"/> which are relatively weak bonds what we called hydrogen bonds <pause dur="0.4"/> which bond across the centre of the molecule <pause dur="1.0"/> always between adenine and thymine <pause dur="0.6"/> and between guanine and <trunc>cytodi</trunc> cytosine <pause dur="1.3"/> with two <pause dur="0.4"/> bonds between adenine and thymine <pause dur="0.4"/> and three bonds <pause dur="0.3"/> between guanine and cytosine <pause dur="0.5"/> that means <pause dur="0.4"/> that a G-C base pair is roughly fifty per cent stronger <pause dur="0.4"/> than a A-T base pair <pause dur="1.7"/> however that's not the only thing that holds the D-N-A molecule together <pause dur="0.8"/> as you see from this <pause dur="0.4"/> picture <pause dur="0.4"/> those D-N-A bases are <trunc>s</trunc> on top of each other <pause dur="0.3"/> stacked on top of each other in fact this bit of the picture shows you that better <pause dur="0.6"/> in this space filling model here we see the bases <pause dur="0.4"/> stacked on top of each other <pause dur="1.0"/> okay those bases being stacked on top of each other <pause dur="0.3"/> they actually interact with each other <pause dur="0.5"/> like this <pause dur="0.3"/> and that gives an

extra <pause dur="0.3"/> layer of stability to the molecule that's called base stacking <pause dur="0.6"/> so base pairing <pause dur="0.3"/> added to base stacking <pause dur="0.4"/> stablilizes the double helix <pause dur="2.9"/> looking at this diagrammatic <pause dur="0.2"/> model of the double helix here <pause dur="2.3"/> some of the details we can count that there are one two three four five six seven eight nine ten bases per turn <pause dur="1.2"/> off the double helix <pause dur="0.6"/> and that amounts to a distance <pause dur="0.4"/> of some three-point-four nanometres <pause dur="2.0"/> and the width of the double helix <pause dur="0.4"/> is about two nanometres <pause dur="2.3"/> a nanometre remember <pause dur="0.3"/> is one <pause dur="0.5"/> times ten-to-the-minus-nine <pause dur="0.3"/> of a metre <pause dur="2.6"/> and the other thing i need to tell you about <pause dur="0.6"/> is if we go back <pause dur="1.3"/> one thing i need to stress and it's one of the mysteries of nucleic acid structure <pause dur="0.6"/> that always mystifies people <pause dur="4.3"/><kinesic desc="changes transparency" iterated="y" dur="3"/>

if we <pause dur="0.4"/> look at that structure <pause dur="0.2"/> as we've draw it here in very simple terms <pause dur="1.1"/> with our <pause dur="0.3"/> sugar <pause dur="0.3"/> phosphate sugar phosphate sugar phosphate backbone <pause dur="1.2"/> okay <pause dur="0.3"/><kinesic desc="writes on transparency" iterated="y" dur="16"/> we have at one end of the molecule here <pause dur="0.7"/> a <pause dur="1.2"/> something with no phosphate on it <pause dur="0.8"/> we conventionally call that the three-prime end <pause dur="0.6"/> because there's a free three-prime carbon <pause dur="0.5"/> stuck here <pause dur="0.7"/> and at the top here we have a free phosphate <pause dur="0.8"/> and that's attached to a five-prime carbon here <pause dur="0.5"/> so we call that end of the molecule the five-prime end <pause dur="1.1"/> okay <pause dur="0.7"/> so just as proteins have two different ends we call them the amino terminus and the carboxy terminus of a protein <pause dur="0.7"/> we talk about the five-prime and the three-prime end of a nucleic acid <pause dur="1.4"/> okay <pause dur="0.9"/> and if we draw a double helix <pause dur="1.2"/><kinesic desc="writes on transparency" iterated="y" dur="30"/> whereas one of the strands is moving from five-prime to three-prime in this direction <pause dur="0.6"/> the other strand <pause dur="0.2"/> is moving from five-prime <pause dur="0.6"/> to three-prime <pause dur="0.5"/> in the opposite direction <pause dur="3.4"/> that is <pause dur="1.3"/> a double helix with its <pause dur="0.7"/> bonds in between <pause dur="1.1"/> we call it an anti<pause dur="0.6"/>parallel <pause dur="0.8"/> double helix <pause dur="2.2"/>

okay because we have two parallel chains <pause dur="0.3"/> one running in one direction <pause dur="0.3"/> and the other one <pause dur="0.2"/> running in the other <pause dur="1.6"/> and half of the problems that people get into thinking about D-N-A <pause dur="0.3"/> has got <pause dur="0.6"/> to do with forgetting <pause dur="0.3"/> that they two run in different directions <pause dur="0.6"/> that was the thing that most people got <pause dur="0.4"/> wrong <pause dur="0.2"/> for instance in the diagnostic test where you were able <pause dur="0.5"/> to <pause dur="0.3"/> to write me <pause dur="0.3"/> the complement of a D-N-A molecule <pause dur="0.3"/> you normally wrote it the wrong way round <pause dur="0.8"/> because the convention is <pause dur="0.3"/> that we always write D-N-A sequences starting at the five-prime and ending at the three-prime <pause dur="0.6"/> so the five-prime is always on the left <pause dur="1.0"/> my right in this case okay and we put out the sequence <pause dur="0.3"/> running <pause dur="0.3"/> from left to right with the five-prime there <pause dur="0.4"/> and the three-prime there <pause dur="4.7"/><kinesic desc="changes transparency" iterated="y" dur="10"/> now that's <pause dur="0.4"/> a molecule of D-N-A <pause dur="1.3"/> what about a molecule of R-N-A <pause dur="0.3"/> what i just wanted to show you <pause dur="0.5"/> as i said they're short <pause dur="0.4"/> and # <pause dur="0.5"/> generally <pause dur="1.4"/> globular <pause dur="1.3"/> and this picture which you haven't got a copy of <pause dur="0.3"/> but you can look up in figure <pause dur="0.4"/> if you see it's in

chapter seventeen of Campbell <pause dur="0.6"/> it's a picture of a T-R-N-A which we'll be talking about <pause dur="0.3"/> again <pause dur="0.5"/> # in the next # <pause dur="0.2"/> part of <pause dur="0.3"/> in the next talk <pause dur="1.0"/> but a T-R-N-A <pause dur="0.5"/> is a short molecule <pause dur="0.6"/> if you could count it's about seventy-five nucleotides long it's trivial compared with the <pause dur="0.5"/> length that we've been talking about in terms of D-N-A <pause dur="1.5"/> okay <pause dur="0.4"/> and as you see it <pause dur="0.2"/> although it's single stranded <pause dur="0.5"/> there's only a single molecule there it coils back on itself <pause dur="0.4"/> making double helical <pause dur="0.3"/> # making base pairs across here <pause dur="0.5"/> and making little bits of double helix <pause dur="0.7"/> as you can see here <pause dur="0.5"/> in this molecule <pause dur="0.3"/> making it in fact <pause dur="0.9"/> almost <pause dur="0.3"/> a a little blob <pause dur="0.2"/> shape like a protein <pause dur="0.5"/> okay <pause dur="0.6"/> so rather than those enormous great molecules three-thousand-million nucleotides long for a piece of D-N-A <pause dur="0.6"/> # <pause dur="0.4"/> we've got something seventy-five base pairs long <pause dur="0.3"/> well <pause dur="0.4"/> R-N-A molecules get larger than that but not a lot larger <pause dur="2.1"/> perhaps a few thousand at most <pause dur="2.2"/> okay so that's looking at the differences between D-N-A and R-N-A <pause dur="0.9"/> and while we were looking at

those differences <pause dur="1.2"/> we <pause dur="0.2"/> # <pause dur="0.2"/> talked a little about <pause dur="0.8"/><kinesic desc="changes slide" iterated="n"/> these forces that bound the D-N-A <pause dur="0.3"/> together <pause dur="1.0"/> okay and you've got that on one of your <pause dur="0.3"/> overheads <pause dur="0.5"/> base pairing <pause dur="0.4"/> with hydrogen bonds two for an A-T base pair three for a G-C base pair <pause dur="0.5"/> and the base stacking <pause dur="0.4"/> bonds which hold <pause dur="0.3"/> the structure together <pause dur="3.5"/> at this point <pause dur="0.9"/> we've talked <pause dur="0.4"/> almost as much as anyone can bear i think about structure <pause dur="0.5"/> so we'll take a two minute break there <pause dur="0.8"/> okay and then we'll go on to talk a bit more about the function of D-N-A </u><gap reason="break in recording" extent="uncertain"/> <u who="nm0238" trans="pause">

<kinesic desc="projector is on showing slide" iterated="n"/> so D-N-A has to function as the genetic material <pause dur="0.9"/> in most <pause dur="0.4"/> cells <pause dur="0.2"/> and most organisms <pause dur="0.8"/> there are a few organisms very simple organisms who use R-N-A as genetic material <pause dur="0.8"/> most obviously some viruses <pause dur="0.6"/> and some rather odd things that plants have called <gap reason="inaudible" extent="1 word"/> <pause dur="2.1"/> but for most organisms D-N-A is the genetic material <pause dur="2.5"/> and that means that he has to do two things <pause dur="3.1"/> it has to act as a store <pause dur="1.5"/> we have to be able to store information <pause dur="1.6"/> and we have to be <trunc>tra</trunc> be able to transmit information <pause dur="1.6"/> and there are basically two modes of transmitting information <pause dur="0.6"/> there's transmitting information from one cell to another <pause dur="1.9"/> and there's what we call expressing information <pause dur="0.6"/> that is <pause dur="0.5"/> moving from genetic information <pause dur="0.6"/> stored <pause dur="0.4"/> to <pause dur="0.2"/> phenotype information <pause dur="0.2"/> expressed <pause dur="2.3"/> which as you remember in the case of <pause dur="0.4"/> molecules is talking about <pause dur="0.3"/> moving <pause dur="0.3"/> from D-N-A <pause dur="0.3"/> to proteins <pause dur="2.9"/> so <pause dur="0.2"/> D-N-A how does it function as an information store we have an

incredibly long molecule <pause dur="1.1"/> a copolymer <pause dur="1.1"/> right <pause dur="0.5"/> which links together <pause dur="1.5"/> four different <pause dur="0.6"/> nucleotides <pause dur="1.0"/> adenine the bases you paired your bases adenine guanine cytosine and <pause dur="0.6"/> thymine <pause dur="1.2"/> A <pause dur="0.5"/> G C and T as we call them <pause dur="1.7"/> okay <pause dur="1.6"/> what we have and people <pause dur="1.1"/> # <pause dur="0.8"/> very soon realized this <pause dur="0.4"/> is basically <pause dur="0.4"/> a <pause dur="0.3"/> piece of linear <pause dur="0.6"/> coded <pause dur="0.2"/> information <pause dur="0.6"/> and the best analogy that i can think of <kinesic desc="holds up strip of cassette tape" iterated="n"/> is magnetic tape <pause dur="1.2"/> okay <pause dur="0.4"/> now you all vaguely know that what we have in magnetic tape is a series of iron atoms <pause dur="0.7"/> okay which are laid out on this plastic tape <pause dur="0.6"/> in some sort of <pause dur="0.2"/> order <pause dur="0.8"/> okay and the <trunc>m</trunc> <pause dur="0.2"/> the magnetics the magnetization of those iron atoms <pause dur="0.7"/> is <pause dur="0.3"/> some indication <pause dur="0.6"/> of <pause dur="0.6"/> information it can be read <pause dur="0.2"/> somehow <pause dur="0.3"/> by a machine <pause dur="0.3"/> and interpreted as sound <pause dur="1.0"/> okay we have a linear <pause dur="1.9"/> # <pause dur="0.4"/> a linear <pause dur="1.0"/> succession of these things which we can pull <pause dur="0.2"/> so we can <pause dur="0.3"/> have these sounds in a linear <pause dur="0.6"/> # arrangement <pause dur="0.2"/> as we like music to be <pause dur="1.3"/> okay <pause dur="0.2"/> well you can imagine D-N-A like this <pause dur="0.3"/> so that the linear sequence of the bases along the strand <pause dur="1.0"/> okay <pause dur="0.6"/> is is the information <pause dur="0.7"/> that is the information

the sequence of bases on a D-N-A strand <pause dur="1.8"/> okay <pause dur="0.7"/> and exactly like this cassette tape <pause dur="2.0"/> you neither you nor i <pause dur="0.8"/> can tell <pause dur="0.9"/> whether <pause dur="0.5"/> this is Cerys Matthews <pause dur="0.2"/> or Dame tiri game Dame <pause dur="0.2"/> Kiri Te Kanawa <pause dur="0.6"/> whether it's <pause dur="0.2"/> Beethoven <pause dur="0.6"/> or <pause dur="0.3"/> # Catatonia <pause dur="1.7"/> # <pause dur="1.3"/> because <pause dur="0.3"/> just like this <pause dur="0.4"/> the information is <pause dur="0.2"/> redundant <pause dur="0.2"/> useless <pause dur="0.4"/> okay <pause dur="0.8"/> this information is no good unless interpreted <pause dur="0.3"/> by some sort of interpreter which in the case of a cassette tape of course <pause dur="0.5"/> is a cassette player <pause dur="0.9"/> but in the case <pause dur="0.3"/> of <pause dur="0.2"/> D-N-A genetic information is the cell <pause dur="1.4"/> okay <pause dur="0.4"/> so that information <pause dur="0.2"/> only has sense in the context of the cell in which it finds itself <pause dur="1.4"/> okay and if you want to think mechanistically <pause dur="0.2"/> you could think of a cell <pause dur="0.3"/> as a cassette player <pause dur="0.4"/> but it's not really helpful <pause dur="0.2"/> i don't think mechanistic <pause dur="0.3"/> analogies really work <pause dur="0.7"/> okay <pause dur="0.2"/> but something needs to <unclear>interpret</unclear> that genetic information that clearly is the cell <pause dur="1.8"/> so the information store consists of the sequence <pause dur="0.5"/> of the bases <pause dur="0.2"/> in the chain <pause dur="1.5"/> the transmission of information as i see it happens in two

ways <pause dur="1.3"/> first of all i'm going to talk about <pause dur="0.2"/> transmission by <pause dur="0.2"/> expression <pause dur="0.6"/> and then we'll talk <pause dur="0.2"/> later <pause dur="0.5"/> about what i've called on this slide <pause dur="0.4"/> maintenance <pause dur="0.3"/> of <pause dur="0.2"/> information but it's also transmission to the next generation <pause dur="0.9"/> okay <pause dur="0.3"/> and its replication <pause dur="3.0"/> in order to <pause dur="0.2"/> look at <pause dur="0.2"/> transmission of information i'm going to go <pause dur="0.4"/> to what <pause dur="0.7"/> i've shown you i think once already <pause dur="0.4"/> which is what <pause dur="0.2"/> # <pause dur="0.9"/> Francis Crick immodestly called the central <kinesic desc="changes slide" iterated="n"/> dogma of molecular biology <pause dur="0.8"/> this little diagram <pause dur="0.5"/> which shows you the information flow inside a cell <pause dur="0.5"/> from the D-N-A store <pause dur="0.6"/> of genetic information <pause dur="0.7"/> through a temporary <pause dur="0.9"/> resting place in R-N-A <pause dur="0.4"/> particularly messenger R-N-A <pause dur="0.9"/> to the protein <pause dur="0.3"/> which is equivalent to the phenotype so from genotype <pause dur="0.4"/> to phenotype within a cell <pause dur="1.0"/> when <pause dur="0.5"/> Crick <pause dur="0.2"/> wrote this out first of all <pause dur="0.3"/> he wrote that diagram with simple arrows on it <pause dur="0.5"/> showing that the information moved from D-N-A to R-N-A to protein <pause dur="2.1"/> okay <pause dur="0.2"/> and that's equivalent to the move from genotype to phenotype <pause dur="2.6"/> now that's <pause dur="0.3"/> although <pause dur="0.3"/> Crick would <pause dur="0.3"/> deny it heartily

that's actually a very simplified form of the central dogma <pause dur="0.4"/> and we'll look <pause dur="0.4"/> at a more complex form in the next lecture <pause dur="1.1"/> okay <pause dur="0.3"/> but that's basically <pause dur="0.2"/> how the information was transmitted <pause dur="0.5"/> inside the cell <pause dur="0.5"/> to interpret <pause dur="0.3"/> the <trunc>ph</trunc> genotype as a phenotype <pause dur="2.0"/><kinesic desc="changes slide" iterated="n"/> what i want to <pause dur="0.6"/> concentrate on <pause dur="0.5"/> in this lecture <pause dur="0.6"/> is the next stage <pause dur="0.5"/> which is replication <pause dur="0.8"/> what the cell has to do <pause dur="3.2"/> because that cell is going to divide <pause dur="0.2"/> and have daughter cells <pause dur="0.3"/> what that cell needs to do <pause dur="0.2"/> in order to pass on that information to maintain <pause dur="0.6"/> a decent store of information <pause dur="0.6"/> in its daughter cells <pause dur="2.8"/> one of the big differences between these two processes transmission <pause dur="0.7"/> and maintenance <pause dur="0.8"/> is that it is much more important <pause dur="0.4"/> for this one to be accurate <pause dur="0.4"/> than it is for this one to be accurate <pause dur="1.3"/> okay <pause dur="0.5"/> when we're trying to maintain the information <pause dur="0.3"/> every time we copy the information if there are mistakes <pause dur="0.8"/> introduced <pause dur="0.4"/> then we've got mutations <pause dur="0.4"/> and we've got a change in our genetic information <pause dur="0.8"/> okay so we want to make absolutely sure if we can

that replication <pause dur="0.2"/> is as accurate as <gap reason="inaudible" extent="1 word"/> be made <pause dur="0.9"/> with transmission of information moving information within a cell <pause dur="0.4"/> from <pause dur="0.2"/> our D-N-A to R-N-A to protein <pause dur="0.3"/> we're not so worried <pause dur="0.2"/> because we're going to throw that R-N-A and that protein away at the end of the day <pause dur="0.2"/> we're going to make new copies <pause dur="0.3"/> and those new copies may be more accurate <pause dur="1.8"/> so although accuracy is the important consideration <pause dur="0.3"/> for both transmission and maintenance it's really the prime <pause dur="0.4"/> problem <pause dur="0.3"/> for maintenance <pause dur="2.4"/> so the process <pause dur="0.5"/> whereby we take <pause dur="0.2"/> a D-N-A double helix and make two D-N-A double helices <pause dur="0.4"/> is the process we refer to as replication <pause dur="0.5"/><kinesic desc="changes slide" iterated="n"/> and that's what i want to spend the rest of this lecture talking about <pause dur="4.6"/>

and D-N-A replication <pause dur="1.3"/> in very simple terms <pause dur="0.2"/> has four important characteristics <pause dur="1.5"/> the first is that it is semiconservative <pause dur="1.7"/> what's that mean <pause dur="0.7"/> one usually makes a political joke here but i won't make a political joke <pause dur="0.5"/> # you can work out a political joke for yourself <pause dur="1.7"/> semiconservative means <pause dur="0.3"/> that if you take a D-N-A double helix <pause dur="0.3"/> and here i'm going to <pause dur="0.4"/> turn to my other favourite model <pause dur="0.3"/> of a D-N-A double helix which is a piece of Velcro <pause dur="2.0"/><kinesic desc="pulls apart piece of Velcro" iterated="n"/> okay <pause dur="0.5"/> the important thing about a piece of Velcro is as you know is that it has two sides <pause dur="0.3"/> which <unclear>better</unclear> bind to each <pause dur="0.3"/> themselves <pause dur="0.2"/> but which bind to each other <pause dur="0.5"/> this entirely mimics <pause dur="0.3"/> the fact that <pause dur="0.2"/> one <pause dur="0.8"/> chain of a D-N-A double helix <pause dur="0.3"/> absolutely specifies and will only bind to # the other chain <pause dur="1.4"/> okay <pause dur="0.4"/> and we say that the chains of a D-N-A double helix are complementary <pause dur="0.3"/> to each other <pause dur="0.4"/>

that's complementary with a E <pause dur="1.1"/> C-O-M-P-L-<pause dur="0.3"/>E-<pause dur="0.4"/>M-E-N-T-R-Y-T-A-R-Y <pause dur="0.5"/> okay they're complementary to each other <pause dur="1.2"/> right <pause dur="0.6"/> we can describe that in very crude terms and say they stick to each other <pause dur="0.4"/> and some people <pause dur="0.3"/> and we do in molecular biology refer to these strands as sticky <pause dur="1.2"/> okay <pause dur="1.4"/> but we've got <pause dur="0.5"/> here's our double helix it's not helical but you could imagine it <pause dur="0.7"/> what happens <pause dur="1.0"/> do we part this double helix <pause dur="1.1"/> make a new chain on here and make a new chain on here and join it up again <pause dur="0.9"/> which would be a conservative model <pause dur="0.2"/> because this helix would remain exactly the same <pause dur="1.7"/> okay <pause dur="1.0"/> or do we <pause dur="0.2"/> throw away both strands of this helix and make a new one well that would be wasteful and clearly we don't do that <pause dur="0.6"/> what we do do <pause dur="0.2"/> is semiconservative replication that is we take these two strands <pause dur="0.5"/> and on each of these two strands we build a new one <pause dur="0.9"/> so for each strand <pause dur="0.5"/> half of it is old there's half of it new <pause dur="0.2"/> and hence semiconservative <pause dur="2.9"/> and that's very clearly shown in the diagram which i think you've got a

version of <pause dur="0.5"/><kinesic desc="changes transparency" iterated="y" dur="8"/> on your handout <pause dur="1.3"/> okay <pause dur="3.6"/> this as i said will be a conservative model where we started with a double helix <pause dur="0.6"/> when we made a new double helix that was entirely new and the old one was kept <pause dur="1.6"/> right <pause dur="1.0"/> that's a conservative model <pause dur="0.5"/> the semiconservative model is where we start with a double helix <pause dur="0.3"/> we part the two strands and make a new one from each <pause dur="0.6"/> and again <pause dur="0.6"/> when we make that one we part the two strands and <pause dur="0.3"/> and # make a new one on each <pause dur="0.2"/> don't worry about the dispersive model i don't think it's worth <pause dur="0.7"/> thinking about at the moment <pause dur="1.5"/> okay <pause dur="0.7"/> so we say that D-N-A <pause dur="0.3"/> synthesis is semiconservative what evidence do we have for that <pause dur="0.9"/> the evidence that we have for that <pause dur="0.4"/> is the evidence of the Meselson-Stahl experiment <pause dur="0.6"/> which again you have <pause dur="0.3"/> on your handout <pause dur="6.6"/><kinesic desc="changes transparency" iterated="y" dur="7"/> okay this was an experiment which was done <pause dur="0.8"/> in # the nineteen-fifties <pause dur="1.0"/> # <pause dur="0.7"/> in which what the # <pause dur="0.3"/> the two <pause dur="0.4"/> authors Meselson and Stahl did <pause dur="0.8"/> was to label <pause dur="0.6"/> the strands of D-N-A this time in the Hershey-Chase experiment remember we <trunc>s</trunc> <pause dur="0.3"/> labelled D-N-A <pause dur="0.4"/> and

labelled protein <pause dur="0.8"/> in the <trunc>men</trunc> <pause dur="0.2"/> Meselson-Stahl experiment what we do <pause dur="0.3"/> what we did <pause dur="0.6"/> was to label the old strands of D-N-A <pause dur="0.3"/> with one isotype <pause dur="0.2"/> not a radioactive one in this case <pause dur="0.7"/> of nitrogen <pause dur="0.8"/> okay and the new strands with the new isotope <pause dur="0.8"/> okay <pause dur="1.4"/> and <pause dur="1.1"/> we then <pause dur="0.2"/> look at <pause dur="0.7"/> the <pause dur="0.3"/> D-N-A molecules that were formed <pause dur="0.6"/> in fact what what they did <pause dur="0.6"/> was to start <vocal desc="clears throat" iterated="n"/><pause dur="0.5"/> with nitrogen fifteen <pause dur="0.9"/> and then they substituted it with nitrogen fourteen <pause dur="0.5"/> nitrogen fourteen is lighter than nitrogen fifteen <pause dur="0.3"/> so the density of the molecule went <pause dur="0.4"/> decreased <pause dur="1.3"/> and they showed that density <pause dur="0.4"/> by <pause dur="0.2"/> running <pause dur="0.6"/> the D-N-A molecules in an ultracentrifuge <pause dur="0.9"/> so here's what they started with in the ultracentrifuge this is heavy D-N-A <pause dur="1.3"/> okay <pause dur="0.8"/> and what you see happening <pause dur="1.0"/> is that as we run <pause dur="0.3"/> through one <pause dur="0.4"/> cell cycle <pause dur="1.1"/> the D-N-A moves from this position <pause dur="0.8"/> to all be at a new position here <pause dur="1.2"/> okay <pause dur="0.3"/> and as we run through a second cell cycle <pause dur="0.3"/> it moves to being at two positions <pause dur="2.1"/> if we go back to our model <vocal desc="clears throat" iterated="n"/><pause dur="2.3"/> we'll see that that's exactly what we

expect <pause dur="0.9"/> from our semiconservative model <pause dur="1.1"/> we start <pause dur="0.5"/> with dark blue heavy <pause dur="0.8"/> and we move through in one <pause dur="0.3"/> cell cycle <pause dur="0.3"/> to everything being a mixture of light <trunc>an</trunc> and dark blue <pause dur="0.3"/> that is the same density <pause dur="0.5"/> whereas in the conservative model <pause dur="0.3"/> we would move <pause dur="0.3"/> from blue <pause dur="0.7"/> to <pause dur="0.4"/> dark blue and light blue two different <pause dur="0.4"/> densities <pause dur="0.8"/> so at the end of the first generation you have two different densities <pause dur="0.5"/> whereas at the end of the first generation here we <pause dur="0.3"/> just have one density <pause dur="0.8"/> at the end of the second generation <pause dur="0.5"/> however in both cases <pause dur="0.6"/> we will have two densities <pause dur="1.2"/> okay <pause dur="1.2"/> <trunc>ar</trunc> in conservative <pause dur="0.5"/> three of them will be light one of them heavy <pause dur="0.5"/> in the case <pause dur="0.2"/> of semiconservative two of them <pause dur="0.5"/> will be mixtures <pause dur="0.3"/> and one of <pause dur="0.2"/> # two of them light <pause dur="0.7"/> and if you again look at the Meselson-Stahl experiment <pause dur="0.6"/> you'll see that that's what happens in the second generation <pause dur="0.4"/> we move from this position here <pause dur="0.3"/> to a mixture of things of that density and some lighter things <pause dur="0.6"/> okay <pause dur="0.6"/> so by measuring the density <pause dur="0.6"/> of D-N-A <pause dur="0.3"/> during the experiment in which we

substituted <pause dur="0.4"/> a light nitrogen isotope for a heavy nitrogen isotope <pause dur="0.5"/> we were able to prove or Meselson-Stahl were able to prove <pause dur="0.3"/> that semiconservative <pause dur="0.2"/> was the correct model <pause dur="0.4"/><kinesic desc="changes slide" iterated="n"/> for D-N-A replication <pause dur="2.8"/> what other characteristics <pause dur="0.5"/> do we need to know about D-N-A replication well first of all <pause dur="0.8"/> does it go all over the place no it doesn't it always starts in one place <pause dur="0.6"/> starts at what we call an origin <pause dur="1.5"/> and in the case of # a bacterial <pause dur="0.4"/> chromosome there is only one origin <pause dur="0.9"/> okay there's only one place where we start and replicate bacterial chromosome <pause dur="0.7"/> in the case of your and our my chromosomes which are infant as we saw <pause dur="0.2"/> a thousand times or so larger <pause dur="1.2"/> # <pause dur="0.4"/> i'm afraid we don't start from one origin but we have many origins otherwise it would take us forever to replicate our D-N-A <pause dur="2.9"/> however from that origin <pause dur="0.5"/> we can very easily show <pause dur="0.3"/> that the D-N-A <trunc>r</trunc> is replicated in both directions <pause dur="1.0"/> okay <pause dur="0.2"/> that replication is bidirectional <pause dur="1.8"/> so if we imagine <pause dur="0.4"/><kinesic desc="changes transparency" iterated="y" dur="5"/> that we're going to start making a piece of D-N-A <pause dur="2.5"/><kinesic desc="writes on transparency" iterated="y" dur="7"/>

so here i have a piece of D-N-A here's a double <pause dur="0.7"/> strand of D-N-A <pause dur="0.7"/> and here is the origin <pause dur="0.8"/> okay <pause dur="0.6"/> obviously the first thing that must happen at the origin is <trunc>w</trunc> <sic corr="we">me</sic> must <pause dur="0.5"/><kinesic desc="writes on transparency" iterated="y" dur="47"/> dissociate the strands like that <pause dur="1.3"/> and you can in fact see that happening in an E-M photograph a little bubble will appear <pause dur="1.5"/> in the D-N-A <pause dur="0.8"/> okay and then we start making D-N-A in both directions that is we make it on this strand <pause dur="0.8"/> okay and we make it on that strand <pause dur="2.8"/> and D-N-A is always made in the same direction <pause dur="1.0"/> it's always made <pause dur="0.2"/> starting <pause dur="0.2"/> with the five-prime of the new strand and moving towards the three-prime of the new strand <pause dur="1.3"/> which since those two strands <pause dur="0.2"/> as i said are antiparallel <pause dur="1.2"/> this strand has a three-prime here and a five-prime there this strand has a three-prime there and a five-prime there <pause dur="1.9"/> okay <pause dur="0.4"/> those two directions will be the opposite directions <pause dur="1.7"/> here we have <pause dur="0.9"/> the snag <pause dur="0.7"/> of D-N-A replication <pause dur="0.7"/> because unless <pause dur="0.6"/> when i replicate bidirectionally i'm going to be satisfied <pause dur="0.7"/> with going this way all

the way round my circular D-N-A <pause dur="0.2"/> if i'm a bacterium <pause dur="0.8"/> okay and come back to meet myself here which will take me a long time <pause dur="0.5"/> and do the same in the opposite direction for the other strand <pause dur="1.2"/> i'm <pause dur="0.2"/> i'm <pause dur="0.6"/> if i'm satisifed with that it will be a very long process <pause dur="0.6"/> and also <pause dur="0.2"/> i will have a single stranded piece of D-N-A hanging around for an awfully long time <pause dur="0.5"/> which you can imagine what it looks like like this you can imagine the <pause dur="0.2"/> problems you'd get into <pause dur="0.9"/> # <pause dur="1.1"/> we need a way of replicating the other strand at the same time <pause dur="2.0"/> and as i've told you <pause dur="0.9"/> we can only replicate D-N-A in one direction <pause dur="1.1"/> and the solution that D-N-A has <pause dur="1.7"/><kinesic desc="changes transparency" iterated="y" dur="3"/> is that although <pause dur="0.3"/> it replicates D-N-A continuously on one strand <pause dur="0.5"/> it <trunc>reputat</trunc> <pause dur="0.2"/> replicates the other strand <pause dur="0.3"/> discontinuously <pause dur="1.9"/> okay <pause dur="1.6"/><kinesic desc="changes transparency" iterated="y" dur="6"/> and that means we make the other strand in fragments <pause dur="2.7"/> so if you imagine the other strand being made <pause dur="0.5"/> what i do <pause dur="0.4"/> is to start here <pause dur="0.7"/> and make a little bit of D-N-A <pause dur="0.8"/> and then i jump back and i start here and make another little bit of D-N-A <pause dur="0.5"/> and then i jump back and

start here and make another bit of D-N-A and so on <pause dur="1.6"/> a motion i've described and it will only mean something to the <pause dur="0.3"/> girls among you i guess as being something like blanket stitch <pause dur="1.1"/> okay in out round the back in out round the back <pause dur="0.4"/> okay <pause dur="1.1"/> those of you who think i've got the nomenclature of the stitch wrong can come up and tell me later but <pause dur="0.5"/> i assure you there is a stitch <pause dur="1.7"/> okay <pause dur="1.1"/> but you see we're going forwards <pause dur="0.3"/> the general direction of synthesis is going in this direction <pause dur="1.1"/> okay but i'm always actually making the molecule in this direction <pause dur="0.5"/> that is the five-prime to three-prime direction <pause dur="0.7"/> i clearly i'm going to make a lot of fragments <pause dur="1.3"/> and those fragments have a special name they're named <pause dur="0.5"/> after the Japanese scientist <pause dur="0.6"/> who first discovered them <pause dur="0.5"/> they're named <pause dur="0.3"/> Okazaki fragments <pause dur="4.1"/><kinesic desc="writes on transparency" iterated="y" dur="4"/> so D-N-A replication is <pause dur="1.1"/> semiconservative <pause dur="0.7"/> we retain one old strand in each new double helix <pause dur="0.7"/><kinesic desc="changes transparency" iterated="y" dur="6"/> it starts from a single place of origin of replication <pause dur="0.9"/> it moves in both directions from that origin <pause dur="0.8"/> moving continuously on one

strand <pause dur="0.3"/> and discontinuously <pause dur="0.4"/> on the other <pause dur="3.2"/> of course what's happening <pause dur="1.2"/> on that strand <pause dur="0.2"/> is something very simple <pause dur="1.4"/> okay and the basic mechanism of D-N-A replication is very simple <pause dur="0.8"/> we have <pause dur="0.2"/> a double stranded helix <pause dur="0.4"/> we part it <pause dur="0.7"/> and then we simply match <pause dur="0.6"/> new bases <pause dur="0.8"/> to replace the new strand so where there's an A we put a T where there's a C we put a G <pause dur="0.4"/> and so on <pause dur="0.5"/> until we get two new strands <pause dur="0.4"/> we're matching <pause dur="0.4"/> bases <pause dur="4.6"/><kinesic desc="changes slide" iterated="n"/> how <pause dur="0.2"/> do we do that <pause dur="0.6"/> how do we do the whole thing what is the mechanism of D-N-A replication <pause dur="4.0"/> and that's where <pause dur="0.8"/> where i want to stop with thinking us through the mechanism of D-N-A replication <pause dur="0.8"/> and we'll then look at the diagram that you've got <pause dur="0.4"/> lastly on your handout which illustrates it <pause dur="0.9"/> so firstly <pause dur="0.2"/> obviously <pause dur="0.2"/> we need to unwind that double helix we need to make our replication bubble as we sometimes call it <pause dur="4.0"/> nature uses two mechanisms to <trunc>underwi</trunc> unwinding the double helix it uses an enzyme which actually physically unwinds it <pause dur="0.6"/> it's called a helicase <pause dur="1.3"/> okay and it actually does that by untwisting <pause dur="0.4"/>

the Watson-Crick double helix <pause dur="2.0"/> and it uses the device of having a protein in the cells <pause dur="0.4"/> which binds strongly to single stranded D-N-A but not to <pause dur="0.3"/> double stranded D-N-A at all a single stranded binding protein <pause dur="0.7"/> okay so as soon as we part the strands <pause dur="0.5"/> this protein binds hard <pause dur="0.3"/> and the <pause dur="0.2"/> the strands are disinclined to come back together <pause dur="0.5"/> then we use two mechanisms <pause dur="0.3"/> for keeping the strands apart <pause dur="3.4"/> then we need to start making some D-N-A <pause dur="0.9"/> and we have a problem <pause dur="1.1"/> we have a problem <pause dur="1.3"/> that problem is <pause dur="2.1"/> clearly we need <pause dur="0.2"/> to get <pause dur="0.3"/> our <pause dur="3.5"/><kinesic desc="puts transparency on top of current slide" iterated="n"/> mechanism right so that we get the right base pairs <pause dur="1.2"/> and the best way to get the right base pairs matching <pause dur="1.0"/> is to have an enzyme <pause dur="0.9"/> which knows <pause dur="0.2"/> roughly <pause dur="0.7"/> how wide a D-N-A double helix is going to be <pause dur="0.5"/> and can fit it <pause dur="0.4"/> okay fit <pause dur="0.2"/> to the helix we've got <pause dur="0.2"/> fit to the distance <pause dur="0.4"/> because an A-T base pair and a C-G base pair are the same size as each other <pause dur="1.2"/> okay <pause dur="1.6"/> and <pause dur="0.6"/> the enzyme can't do that <pause dur="0.3"/> at the same time <pause dur="0.5"/> as starting a strand on its own <pause dur="1.8"/> the enzyme which makes D-N-A <pause dur="0.2"/> will not start a strand on its own <pause dur="0.9"/> so it needs to be helped <pause dur="0.9"/> and it needs to build a primer first <pause dur="1.5"/> okay <pause dur="0.6"/> and that primer's always made of R-N-A <pause dur="1.3"/>

okay so we have to first in order to make D-N-A make some R-N-A <pause dur="2.1"/><kinesic desc="changes transparency" iterated="y" dur="2"/> and what this means basically is going to this <pause dur="0.7"/><kinesic desc="writes on transparency" iterated="y" dur="30"/> going over here <pause dur="0.6"/> let's imagine we have our <pause dur="0.6"/> piece of D-N-A <pause dur="1.0"/> okay <pause dur="0.3"/> imagine this is the five-prime of it and this is the three-prime of it and we're going to make <pause dur="1.0"/> # <pause dur="1.0"/> some D-N-A here we're at the origin <pause dur="0.7"/> we start with a piece of R-N-A <pause dur="0.9"/> which <pause dur="1.0"/> bonds like that <pause dur="0.9"/> okay made from five-prime to three-prime <pause dur="1.7"/> and then the enzyme which makes D-N-A takes over from this point <pause dur="0.7"/> and makes D-N-A <pause dur="0.4"/> in the right direction <pause dur="1.5"/> okay <pause dur="1.7"/> so at the beginning <pause dur="1.2"/> of <pause dur="0.2"/> our <pause dur="0.2"/> D-N-A we have <pause dur="0.3"/> a combination of a primer made of R-N-A <pause dur="1.7"/> and an old strand <pause dur="0.4"/> of D-N-A which we're using <pause dur="0.2"/> to read <pause dur="0.4"/> the correct sequence which we call a template <pause dur="0.9"/> okay so at the beginning we have a template and a primer <pause dur="6.4"/> so we start the chain with R-N-A <pause dur="0.2"/> we make a primer <pause dur="0.4"/> and then we continue D-N-A synthesis <pause dur="0.9"/> on the continuous strand that we call

the leading strand <pause dur="1.2"/> okay because it's always slightly ahead <pause dur="0.2"/> of the other strand in making D-N-A <pause dur="1.3"/> okay <pause dur="0.3"/> and on the other strand the lagging strand as we call it 'cause it is slightly behind <pause dur="0.7"/> okay <pause dur="0.7"/> we make those fragments those Okazaki fragments and we need one more process to go on and that is we need to join the fragments together <pause dur="1.2"/> okay so we need a ligase <pause dur="0.3"/> a joining together enzyme <pause dur="0.3"/> to join the fragments together <pause dur="2.0"/> so we can incorporate all that information <kinesic desc="changes transparency" iterated="y" dur="7"/> about the mechanism of replication <pause dur="0.6"/> on the diagram here <pause dur="0.6"/> that i've given you a copy of <pause dur="2.4"/> okay which gives you a brief summary <pause dur="0.4"/> of D-N-A replication here's the parental D-N-A which has started <pause dur="0.7"/> it's being unwound at this point <pause dur="0.7"/> and there are single stranded binding proteins these are the pink fingers <pause dur="0.6"/> binding to the single stranded D-N-A <pause dur="2.1"/> all right <pause dur="0.2"/> then we <pause dur="1.0"/> we have D-N-A being made <pause dur="0.4"/> continuously in this direction <pause dur="0.9"/> okay by the enzyme

which makes D-N-A the D-N-A polymerase <pause dur="1.3"/> and on this <pause dur="0.3"/> strand <pause dur="0.4"/> we're making bits of D-N-A <pause dur="1.7"/> but starting with R-N-A primers <pause dur="0.6"/> to make our Okazaki fragments <pause dur="0.6"/> we're then extending our Okazaki fragments <pause dur="0.9"/> and in the end <pause dur="0.6"/> here's the D-N-A ligase enzyme joining two Okazaki fragments together <pause dur="1.1"/> so we unwind <pause dur="0.9"/> continuously make D-N-A on this strand <pause dur="0.5"/> five-prime to three-prime direction <pause dur="0.4"/> we discontinuously make it on this strand starting with an R-N-A primer <pause dur="1.5"/> and then making our D-N-A until it bumps into the next one basically it just falls off and it bumps in <pause dur="0.8"/> and then we have to join up our two Okazaki fragments <pause dur="0.3"/> using a ligase <pause dur="1.1"/> so that is the basic mechanism <pause dur="0.3"/> of D-N-A replication and that's where we shall end <pause dur="0.6"/> this first <pause dur="0.5"/> # <pause dur="1.1"/> talk for this afternoon <pause dur="0.7"/> okay <pause dur="0.3"/> i'll be putting out some more handouts for you for the second talk in just a second <pause dur="0.8"/> we'll take a five minute break