transcription (genetics)

3

Post-Transcriptional Processing

•Only in the Nucleus for Eukaryotes •Primary transcript processed in 3 ways: –1. ADDition of nucleotides –2. DELETion of nucleotides –3. Modification of Nitrogenous Bases •5’ cap and 3’ Poly A tail •snRNP and the Spliceosome of Doom! –INtrons = IN nucleus –EXtrons = EXit the nucleus

DNA TECHNOLOGY

Clone Library = plasmid and replication

Polymerase chain reaction (PCR) : ‘fast’ cloning

•Heat to denature •Mix with primers, let cool = primers hybridize •Add polymerase to amplify complementary strands

Southern Blot

•1. Chop up DNA •2. Efield to spread out pieces by SIZE •3. Blot it! •4. Add Radioactive DNA or RNA Probe •5. Visualize on radiographic film  GENETIC CODE •Degenerative – more than one series of nucleotides may code for ANY A.A. •Unambigous = one series of nucleotides = one A.A. •Universal code! •START! AUG •STOP! UAA, UAG, UGA •4^3 = 64 –Ex. protein of 100 A.A. = there are 20^100 possible amino acids sequences for the protein 
DNA transcription

snRNA and nuclear proteins form snRNP’s [pronounced like snurps] that join protein complexes to form the complex molecular machine called splicisomes which remove introns from transcribed Pre-mRNA

Transcription factors bind to a region of the DNA called the promoter, which identifies the start of the gene, which strand is to be copied, and the direction in witch it is copied.

RNA polyemerase then binds to the transcription factors and promoters

(in prokaryotes there are no transcription factors so RNA polymerase binds directly to the promoter)

RNA polymerase unwinds DNA then aranges the complimentary nucleotides 

THE DIRECTION OF SYNTHESIS IS 5’ TO 3’

Then transcription stops:

in prokaryotes there is a termination sequence in the DNA that indicates where it will stop

In eukaryotes transcription stops after the polyadenylation signal

Despite their diversity in shapes and forms, the majority of Pokemon species seem to have seperate sexes, and reproduce via sexual reproduction. 

Despite having a very expansive genome and such radically different morphologies between eachother, Pokemon as a whole only have the amount of genetic diversity between eachother as just a single genus of animals. The genome of an Onyx compared to a Weepinbell is as different as that between a  husky and a coyote. A “species” of Pokemon is not determined by its nuclear DNA, but rather by specialized organelles outside the nucleus. These organelles seem to heavily regulate transcription of genetic information, and turn “off” large sections of the genome  and control which genes are expressed. 

Like how Mew contains “the genetic code of all pokemon”, so do all regular Pokemon too. The difference between a Pikachu and a Meowth isn’t nessesarily the differences between their genomes, but rather which parts of their genome do they express.

The organelles responsible for these differences in gene expression are also strictly inherited from the mother, in her egg cells (much like how we inherited mitochondria from our mother). This means while a Pokemon who’s mother is a Meowth and father is a Pikachu does have half the genes of both it’s parents, it will only inherit the organelles from it’s mother. Hence it’s “species” will be that of it’s mother, and will hatch as a Meowth regardless of it’s father.

So yes, using artificial insemination you can breed a Skitty and a Wailord together, but the babies will always come out as the mother’s species as opposed to some sort of hybrid that would kill a female skitty to produce.

mcknighty9  asked:

Teach me a zoologist lesson!

I would like to introduce you to Oikopleura

Not only does it have a smashing name, it is one of my favourite animals (despite looking like something from an alien movie)

It is a master predator of the tiniest of plankton, down to nanoplankton (that is, bacterial plankton). Every four hours, it builds itself a complex house (house is the correct scientific terminology) out of a gelatinous material. The house has meshes of varying thicknesses, one to keep out big particles that it can’t eat, and one to filter out smaller particles, which it does eat, carried to it’s stomach along mucus threads. Swimming like a tadpole, it pushes it’s house through the water column, filtering out it’s dinner as it goes (like this)

After about 4 hours, it sheds it’s house (it’s large filter will be clogged by that stage) and builds a new one. The old house sinks to the bottom of the sea as ‘marine snow’ and eventually collects as a marine ooze at the bottom of the sea floor, along with other biological droppings, and organic matter. Together, Oikopeurids contribute hugely to carbon sequestration on the sea floor.

Another cool think about Oikopleura, is that it is more related to you or I than you might think. Oikopleura is a Tunicate, the Subphylum more commonly known as Ascidians, or more common still, the Sea Squirts (see below)

Sea squirts lead a simple life, sitting in one spot, filtering seawater for food out of one opening, and expelling that water out of the other. However these primitive jelly looking things are more related to us, to your cat, your lizard, that bird, a fish etc., much more so than molluscs, arthropods, jellyfish - pretty much any invertebrate is. 

Sea Squirts are Chordates. Yes, you heard right, that is our phylum, the phylum of the vertebrates. Though their adult stage looks alien, their larval stage, is much more familiar

Their tadpole like larvae are free swimming. Whilst they don’t have a spine per se, they do have a notochord, a flexible cartilage like rod that runs along their body and post-anal tail, a kind of primitive spine predecessor that all vertebrates possess when we develop as embryos. Tail muscles attach to the notochord, much as tadpole tail muscles attach to a vertebral column, and allows the larvae to swim in that same undulating fashion. They also possess a number of characteristic chordate features - a hollow dorsal nerve cord, pharyngeal slits (so, gill slits essentially. We still even have them as early embryos), an endostyle (a gland that produces mucous and deals with iodine metabolism. It is the predecessor to our thyroid gland) and a post anal tail. 

Sea squirt larvae, once they hatch, swim around looking for a place to settle. When they find a nice looking spot, they stick themselves to the rock, and undergo metamorphosis, changing to their more simpler adult looking form. The genetic pathways, transcription factors, and other proteins that are active during the formation of the adult sea squirt heart and pharynx remain relatively unchanged during the embryonic development of those areas in vertebrates, which of course includes us (these ancient pathways are the focus in modern heart developmental biology, very relevant to tackling congenital heart defects). 

However, Oikopleura is different. It belongs to a group of Tunicates known as the Larvaceae, a group characterised by their retention of their larval form when they mature as adults, i.e no metamorphosis. This is known as neoteny, or pedomorphosis, when an individual can become sexually mature whilst retaining their juvenile form. Another example of this would be the Axolotls, who as adults, retain juvenile features such as gills, and don’t undergo full metamorphosis to an adult, semi-terrestrial salamander like form. And thus, Oikopleura lives out it’s adult life, retaining a larval ascidian body. 

Now here’s where it gets interesting. There is a theory that suggests that the first predecessors of the vertebrates, i.e. the predecessors to the first “fish” may  have been a neotenous tunicate, like Oikopleura. It would have had all the basic requirements and features for an ancient chordate and vertebrate predecessor, and by investing in a more active swimming lifestyle, it is not hard to see it evolving a more sophisticated pharynx for filter feeding and a more muscular hydrodynamic body for swimming, as in the earliest true chordate fossils, our ancestors from ~520 MILLION years ago, like Pikaia

or what is coined sometimes as the first “fish”, Haikouicthyes

So, TL:DR - Something very like the tiny Oikopleura may have been the ancestor to all vertebrates!!

anonymous asked:

Can you please explain how electron orbitals work? Like what are they why are they all weird shaped and what the heck are nodes? Also- bonus question: clarify how electrons act like waves and particles

I’m not a quantum chemist in any way shape or form, and I failed pretty hard at doing basic tasks like making buffer today so I may not be the best source of information here, but I’ll do my best to answer your question.

Atomic orbitals are probability density functions, which means that they represent the area where an electron is most likely to be found, (if you want to think of an electron as a discrete particle with a definite location, which isn’t actually accurate but is a nice approximation that makes everybody’s head hurt a little less, so let’s go with that.) The nodes then, are the places that the electron is definitely not, like never ever. A handy way to remember this is nodes = No damn electrons. 

The shapes happen because orbitals behave like waves, so they add and subtract from each other based on their signs (positive and negative, not pisces and gemini, the reason that they have said signs is as mysterious to me as why people care about the zodiac, but has more math involved).

This bit is pretty opaque to me because I spend my days thinking about things like gene transcription and worm genetics and not quantum mechanics, but basically each orbital is described by a set of quantum numbers denoting energy (n), angular momentum (l), axial (?) orientation (ml) and spin (ms), which taken together describe their shape and size based on the Schroedinger equation, but the one that is most important for the shape is angular momentum (l). Why they are shaped the way they are is due to the way that the Schroedinger equation is solved for those numbers and has to do with oscillations and shit, iirc, but basically if you do the math it makes sense. If not, you accept that they look the way they do and don’t judge the d and f orbitals for their weird shapes. 

(mj-the-scientist could probably explain all of this better because this is sort of her field, so yeah, please correct my many mistakes, I am a humble biologist)

As for why electrons (and all particles really) act as both waves and particles? The best allegory I’ve got is this:

It’s like how science-jesus is both fully human scientist and fully divine scientist while also only one single scientist. The way that that adds up has been the subject of much ecclesiastical debate, has lead to schisms in the science church, and makes your head hurt if you think too much about it, but is ultimately because a bunch of old guys said so a long time ago. In our case, the old guys are math.