an autodidact meets a dilettante…

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Posts Tagged ‘DNA

a DNA dialogue 3: two anti-parallel strands

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but why the twist? – we don’t know yet

Jacinta: Ok so these two strands of DNA are described as anti-parallel. Is this just intended to confuse us?

Canto: Apparently not, in fact it’s quite essential. The useful q&a site Quora has good info on this, and understanding it in all its complexity should help us to understand DNA general – it’s one of a thousand useful entry points.

Jacinta: Yes, and I’ll try to explain. It became clear to us last time that the strands or ribbons twisted round in a double helix, called the backbone of the molecule, are made from phosphate and deoxyribose sugar, covalently bonded together. That means tightly bonded. Between the two strands, connecting them like ladder rungs, are nitrogenous bases (this is new to us). That’s adenine, thymine, guanine and cytosine, bonded together – A always to T, and C to G – with weak hydrogen bonds. We’ll have to look at why they must be paired in this way later.

Canto: It’s called Chargaff’s base pairing rule, which doesn’t tell us much.

Jacinta: And, according to a respondent from Quora, ‘the two strands of DNA are anti-parallel to each other. One of them is called leading strand, the other is lagging strand’. But I don’t quite get this. How are there two strands of DNA? I thought there was one strand with two sugar-phosphate backbones, and a rung made up of two – nitrogenous nucleobases? – weakly connected by hydrogen bonds.

Canto: I think the idea is there are two strands, with the attached bases, one next to another on the strand, and weakly attached to another base, or set of bases each attached to another phosphate-sugar backbone. As to why the whole thing twists, rather than just being a straight up-and-down ladder thing, I’ve no idea. Clearly we’re a couple of dopey beginners.

Jacinta: Well, many of the Quora respondents have been teaching molecular biology for years or are working in the field, and just skimming through, there’s a lot be learned. For now, being anti-parallel is essential for DNA replication – which makes it essential to DNA’s whole purpose if I can call it that. I’ll also just say that the sugars in the backbone have directionality, so that the way everything is structured, one strand has to go in the opposite direction for the replication to work. If for example the strands were facing in the same direction, then the base on one side would connect to a hydrophobic sugar (a good thing) but the base on the other side would be facing a hydrophilic phosphate (a bad thing). Each base needs to bond with a sugar – that’s to say a carbon atom, sugar being carbon-based – so one strand needs to be an inversion of the other. That’s part of the explanation.

Canto: Yes, I find many of the explanations are more like descriptions – they assume a lot of knowledge. For example one respondent says that the base pairs follow Chargaff’s rule and that means purines always pair up with pyrmidines. Not very helpful, unless maybe you’re rote-learning for a test. It certainly doesn’t explain anti-parallelism.

Jacinta: Well, although we don’t fully understand it yet, it’s a bit clearer. Anti-parallelism is an awkward term because it might imply, to the unwary, something very different from being parallel. The strands are actually parallel but facing in the opposite direction, and when you think about the structure, the reason for that becomes clearer. And imagining those backbone strands facing in the same direction immediately shows you the problem, I think.

Canto: Yes and for more insight into all that, we’ll need to look more closely at pyrmidines and purines and the molecular structure of the backbone, and those bases, and maybe this fellow Chargaff.

References

https://www.quora.com/Why-are-DNA-strands-anti-parallel

https://slideplayer.com/slide/13304243/

Written by stewart henderson

January 21, 2020 at 2:38 pm

A DNA dialogue 2: the double helix

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Canto: Ok we talked about base pairs at the end of dialogue 1. A (nucleo)base pair is, duh, a pairing of nucleobases. There are four types of base in DNA – adenine and thymine, which always pair together, and the other pairing, cytosine and guanine.

Jacinta: Please explain – what’s a nucleobase, what do they do, and why do they come in pairs?

Canto: Well, let’s see, how do we begin… DNA stands for deoxyribonucleic acid…

Jacinta: So it’s an acid. But bases are like the opposite of acids aren’t they? So how can an acid be constructed of its opposite?

Canto: Look, I can’t answer that right now – I haven’t a clue – but let’s keep investigating the structure and function, and the answers might come. So, you’ll know that there was a battle in the 1950s to elucidate the structure of DNA, and it was found to form a double helix two strands of – I don’t know what – connected to each other in a twisted sort of way by, I think, those base pairs connected by hydrogen bonds. Anyway, here’s a fairly typical explanation, from Nature Education, which we’ll try to make sense of:

The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together. Each DNA strand within the double helix is a long, linear molecule made of smaller units called nucleotides that form a chain. The chemical backbones of the double helix are made up of sugar and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate backbones. The two helical strands are connected through interactions between pairs of nucleotides, also called base pairs. Two types of base pairing occur: nucleotide A pairs with T, and nucleotide C pairs with G.

Jacinta: So I think I have a problem with this description. I think I need a picture, fully labelled. So the two strands themselves are made up of nucleotides, and the connections between them are made up of bonded sugar and phosphate molecules? But the strands are connected, via sugar and phosphate, in particular ways – ‘through interactions’ – which only allow A to pair with T, and C to pair with G?.

Canto: I think that’s right. Maybe we can find a picture.

Jacinta: Ok, so we got it completely wrong. The backbone, of sugar-phosphate, is the outer, twisted strand, or two of them, like the vertical bars of a twisted ladder, or the toprails of a spiral staircase, and the base pairs are like the stairs themselves, made of two separate parts, the bases, bonded together by hydrogen…

Canto: Forget the description, the picture above is worth all our words. It also tells us that the DNA molecule is around 2 nanometres wide. That’s two billionths of a metre. And 3.4 nanometres long for a full twist of the double helix, I think.

Jacinta: Whateva. There’s also this claim that the two strands are ‘anti-parallel’. It looks to me as if they’re simply parallel, but twisted. What does this mean? Is it significant?

Canto: I don’t know – maybe we’ll find out next time. I’m already exhausted.

Jacinta: …….

Written by stewart henderson

January 16, 2020 at 5:13 pm

Posted in biochemistry, DNA, science

Tagged with , ,

A DNA dialogue 1: the human genome

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what genomics tells us

Canto: I’m often confused when I try to get my head around all the stuff about genes and DNA, and genomes and alleles and chromosomes, and XX and XY, and mitosis and meiosis, and dominant and recessive and so on. I’d like to get clear, if only I could.

Jacinta: That’s a big ask, and of course we’re both in the same boat. So let’s use the magical powers of the internet to find answers. For example, here’s something that confuses me. The Human Genome project, which ended around the year 2000, involved a mapping of the whole human genome, and that includes coding and non-coding genes, and I think it was found to contain 26,000 or so – what? Letters? Genes? Coding genes? Anyway there’s a number of questions there, but they’re not the questions that confuse me. I don’t get that we now, apparently, have worked out the genetic code for all humans, but each of us has different DNA. How, exactly, does our own individual DNA relate to the genome that determines the whole species? Presumably it’s some kind of subset?

Canto: Hmmm. This article from the Smithsonian tells us that the genetic difference between human individuals is very tiny, at around 0.1%. We humans differ from bonobos and chimps, two lineages of apes that separated much more recently, by about 1.2%….

Jacinta: Yes, yes, but how, with this tiny difference between us, are we able to use DNA forensically to identify individuals from a DNA sample?

Canto: Well, perhaps this Smithsonian article provides a clue. It says that the 1.2% difference between us and chimps reflects a particular way of counting. I won’t go into the details here but apparently another way of counting shows a 4-5% difference.

Jacinta: We probably do need to go into the details in the end, but clearly this tiny .1% difference between humans is enough for us to determine the DNA as coming from one individual rather than 7 to 8 billion others. Strangely enough, I can well believe that, given that we can detect gravitational waves and such – obviously using very different technology.

Canto: Yeah the magic of science. So the Human Genome Project was officially completed in April 2003. And here’s an interesting quote from Wikipedia:

The “genome” of any given individual is unique; mapping the “human genome” involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.

Of course it would have to be a mosaic, but how can it represent the whole human genome when it’s only drawn from a small number? And who were these individuals, how many, and where from?

Jacinta: The Wikipedia article does give more info on this. It tells us that the project isn’t really finished, as we’ve developed techniques and processes for faster and deeper analyses. As to your questions, when the ‘finished’ sequencing was announced, the mosaic was drawn from a small number of anonymous donors, all of European origin.

Canto: But we all originated from Africa anyway, so…

Jacinta: So maybe recent ‘origin’ isn’t so important. Anyway, that first sequencing is now known as the ‘reference genome’, but after that they did sequence the genomes of ‘multiple distinct ethnic groups’, so they’ve been busy. But here are some key findings, to finish off this first post. They found some 22,300 protein-coding genes, as well as a lot of what they used to call junk DNA – now known as non-coding DNA. That number is within the mammalian range for DNA, which no doubt surprised many. Another blow for human specialness? And they also found that there were many more segmental duplications than expected. That’s to say, sections of DNA that are almost identically repeated.We’ll have to explore the significance of this as we go along.

Canto: Yes, that’s enough for starters. Apparently our genome has over 3 billion nucleobase pairs, about which more later no doubt.

References

http://humanorigins.si.edu/evidence/genetics

https://en.wikipedia.org/wiki/Human_Genome_Project

Written by stewart henderson

January 13, 2020 at 11:48 pm

epigenetics and imprinting 4: the male-female thing

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Gametes are gametes because of epigenetic modifications in their pro-nuclei, but they have to lose these modifications, or transform them, when they come together to form zygotes. The male pro-nucleus DNA methylation is stripped away immediately after sperm penetrates egg. The egg pronucleus undergoes the same process, but more gradually. It’s like a wiping away of epigenetic memory, creating totipotency, which becomes a more limited pluripotency as the blastocyst, with its inner cell mass (ICM), forms. 

The ICM cells begin differentiating through the regulation of some key genes. For example, a gene codes for a protein that switches on a set of genes, which code for proteins in a cascading effect. But it’s not quite a matter of switching genes on or off, it’s rather more complex. The process is called gene reprogramming, and it’s of course done effortlessly during every reproductive cycle. Artificial reprogramming of the kind carried out by Yamanaka and others, an essential part of cloning, hasn’t come close to this natural process that goes on in mammals and other species every day.

Clearly, though the epigenetic reprogramming for the female pronucleus is different from that carried out more swiftly in the male. As Carey puts it, ‘the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily.’ Human researchers haven’t been particularly successful in reprogramming an adult nucleus by various methods, such as transferring it to a fertilised egg or treating it with the four genes isolated by Yamanaka. The natural process of gene reprogramming eliminates most of the epigenetic effects accumulated in the parent genes, but as the reprogramming is a different process in the male and female pro-nucleus, this shows that they aren’t functionally equivalent. There is a ‘parent-of-origin effect’. Experiments done on mice to explore this effect found that DNA methylation, an important form of chromatin modification (and the first one discovered), was passed on to offspring by the female parent. That’s to say, DNA from the female was more heavily methylated than that from the male. Carey describes the DNA as ‘bar-coded’ as coming from the male or the female. The common term for this is imprinting, and it’s entirely epigenetic.

Imprinting has been cast by Carey, and no doubt others, as an aspect of the ‘battle of the sexes’. This battle may well be imprinted in the pronuclei of the fertilised egg. Here’s how Carey puts the two opposing positions:

Male: This pregnant female is carrying my genes in the form of this foetus. I may never mate with her again. I want my foetus to get as big as possible so that it has the greatest chance of passing on my genes.

Female: I want this foetus to pass on my genes. But I don’t want it to be at the cost of draining me so much that I never reproduce again. I want more than this one chance to pass on my genes.

So there’s a kind of balance that has developed in we eutherian mammals, in a battle to ensure that neither sex gains the upper hand. Further experiments on mice in recent times have explored how this battle is played out epigenetically. I’ll look at them in the next post in this series.

Reference

The Epigenetics Revolution, by Nessa Carey, 2011

Written by stewart henderson

January 9, 2020 at 10:50 am

modern humans are getting less modern, in unexpected places

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Taken from the website of Science magazine

In recent years we’ve been almost overwhelmed by paleontological discoveries (and re-analyses of earlier discoveries), from giant worm jaws to a new subclass of cephalopod to a new semi-aquatic non-avian dinosaur to the oldest fossils yet found of that strange species, Homo sapiens. 

I’ve decided to focus on the last example, for now. Homo sapiens fossils discovered at Jebel Irhoud in Morocco in the sixties, and long thought to have been some 40,000 years old, came under increasing ‘suspicion’ from palaeontologists, beginning in the eighties, due to various curious anomalies. More intensive searching at the Jebel Irhoud site recently has led to a wealth of discoveries, ‘including skull bones from five [human-like, though with a different brain-case, especially at the back] individuals who all died around the same time’. And thanks to the new thermoluminescence dating technique, which is applied to heated or burned substances (it’s a measure of accumulated radiation), a date of 300,000 years was calculated for the tools found near the fossils, and by association for the fossils themselves. This makes them over 100,000 years older than those found in Ethiopia. The Ethiopian fossil discoveries gave rise to the idea that ‘modern’ humans began life in a small region of East-Central Africa and gradually spread, but the revelation about the Moroccan fossils means a revision, or overturning, of that hypothesis.

You’ll notice I’ve put modern in skeptical quotes. It seems to me nobody will agree on what a modern human really is, or whether it’s decided entirely on anatomical or physiological features. If you found yourself suddenly transported to the days of Sargon and the Akkadian civilisation, only 4,500 years ago, you probably wouldn’t have the impression you were living among modern humans – depending on how prepared you were for the culture shock. Of course, paleontologists would have different measures for modernity – brain size, skeletal features and such – but these are necessarily imprecise given individual variation and the sparsity of really good fossils. And there’s also the matter of incremental, barely discernible change. For example, our 300,000-year-old Jebel Irhoud specimens are, perhaps, the oldest known modern human specimens, but it would be silly to argue that their parents weren’t just as modern – and what of their grandparents? And in this way we can go back another 10,000 years, or maybe 50,000, without seeing much difference. This has always been the most difficult thing to get my head around, not only for H sapiens but for any species. When does Australopithecus afarensis start/stop being Australopithecus afarensis? When did a chimp distinguish herself from a bonobo, and when did they both get differentiated from their predecessor? Are we taking hard and fast taxonomy too seriously? Maybe I’ll return to that some time…

Meanwhile, another recently revealed discovery has added to the ‘out of Africa’ confusion, which many thought was becoming less confused, with something like a consensus that H sapiens  emerged from Africa between 70 and 100 thousand years ago and dispersed globally, with the oldest Australian human possibly dating back as far as 65,000 years.

The discovery of a human jawbone and teeth in Israel that date back nearly 200,000 years has messed up that simplifying story, and it’s only one of a number of finds that are making the experts get confused – and excited – again. The jawbone find, combined with sophisticated tools and weaponry, is solid evidence of H sapiens coming out of Africa much earlier, and perhaps on an irregular basis depending on climatic conditions and resources. Human teeth found in China, and human fossils in Sumatra, dating to at least 70,000 years ago, tend to confirm this hypothesis. Other fossil discoveries in Israel are complicating the picture. The Eastern Mediterranean seems to have been a crossroads where various early human species may have interacted.

These new discoveries appear to confound the genetic evidence that we’re all related to an out-of-Africa population that emerged well under 100,000 years ago, but it seems these early populations died out or returned to Africa.

Yet there are so many mysteries still to solve. What about the strange Denisovans? We have so little fossil evidence, yet enough to map almost the entire nuclear and mitochondrial genome – a testament to modern technology. Analysis of their mtDNA suggests that they migrated out of Africa much earlier than the modern humans above-mentioned, but later than H erectus. They apparently branched off from the human line 600,000 years ago, and from Neanderthals about 400,000 years ago. The fullness and fascinating richness of the Wikipedia article on the Denisovans, garnered from such minute fossil evidence, is a source of great wonder to me. The specimens (of four distinct Denisovans) were well preserved due to the icy temperatures in the Siberian cave, near the Mongolian-Chinese border, where they were found. The finger bone, dated to about 40,000 years BP (Before Present, a new designation to me, and a welcome one), has yielded both mitochondrial and nuclear DNA, which has shown the Denisovans to be distinct from both Neanderthals and modern humans, and that they share a common ancestor with Neanderthals. Other excavations of the cave show that it was inhabited at least 125,000 years ago. mtDNA analysis has apparently revealed that the three, H sapiens, Denisovans and Neanderthals, shared a common ancestor about 1 million years ago. I’m writing these facts, if they are facts, as I find them, while wondering what they mean, and especially how the evolutionary tree can be visualised, but it’s pretty difficult, especially when you consider interbreeding. Looks like I’ll have to write and do the research for half a dozen posts before I start to get it straight in my own head. Anyway, here’s one interesting chart I’ve found.

 

There are clearly more mystery hominids to be found, to fill out the complicating picture. And of course I’ve mentioned the genetics and genomics only in passing, but again it’s astonishing what they can find these days by comparing these genes with what we know of some modern human populations. For example, studies of the Denisovans genome found ‘a region around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude’, already known from analysis of modern Tibetan genes.

Hoping to keep myself up to date with all this, if I don’t get too distracted by the zillions of other fields of enquiry worth keeping up with…

References

https://www.theguardian.com/science/2018/jan/25/oldest-known-human-fossil-outside-africa-discovered-in-israel

https://www.theatlantic.com/science/archive/2017/06/the-oldest-known-human-fossils-have-been-found-in-an-unusual-place/529452/

https://en.wikipedia.org/wiki/Denisovan

 

All the excitation about Trump having tried to sack Mueller annoys me because it makes me – well, too excited. I have to learn to be patient. The Mueller enquiry will end when it does, and it’s sure to end dramatically. Still, I hunger for another indictment, or equivalent headline. One point worth worrying about though, is what happens when Trump goes? The whole administration should go, but that’s not what happens in the US. No snap elections, no double dissolution. Another weakness of the Presidential system, it seems to me. In the US, you vote for a personality, and that personality gets to build a team around him (it’s always been a bloke), whereas in most advanced western nations, the country’s leader has risen through the ranks of the team, much like the captain of a soccer team, who’s given the captain’s armband, not because she’s the best player – though she quite often is – but because she’s the most inspiring leader. If that captain falls afoul of the law, another competent team member can take on the job. In the case of the US Presidency, the team is tainted by the captain’s failings because he’s personally chosen the lot of them – in this case largely because of their political ignorance, which he regards as a positive.

 

Written by stewart henderson

January 29, 2018 at 10:31 pm