This Is Me... Studying

Let's talk about DNA! DNA (deoxyribose nucleic acid) are polymeres of nucleotides. Nucleotides are made up of a nitrogenous base, pentose monosaccharide and phosphate ion. How are they all connected? Well, good thing you asked or you might have failed your exam. The pentose monosaccharide and nitrogenous base are joined through a condensation reaction to form a glycosidic bond. This occurs on the 1' carbon. On the 5' carbon, the phosphate joined through a phosphodiester bond. The nucleotides polymer their shit up by the phosphate of one nucleotide joining to the 5' carbon of the next pentose monosaccharide. This create a 5' and 3' end with the 5' end having a phosphate group attached and the 3' end having... nothing? Just a pentose monosaccharide? Nfi. So, we have these DNAs which are secretly double helices. We have two strands of nucleotides which join up through H-bonds between the nitrogenous bases. The bases are what characterise the DNA and they always have a complementary partner. There are 4 bases found in DNA - A, C, G, T (I forget what the letters stand for... Guanine? Thyamine? Ayayayamine? Cuntnine?). A goes with T, C goes with G so those pairs are always joined by H-bonds in the double helix. Furthermore, we can divide the bases up into being either pyrimidine (single) or purine (double). In a base pair, there must be one pyrimidine and one purine. A and G are purines, C and T are pyrimidines. (I had to check my notes for that... I will fail the exam) How does all this shit fit in the nucleus of the cell? The DNA has to be all nicely packaged up. The DNA double helices coil around an octameric histone core (8 protein core) due to electrostatic charges between the negatively charged DNA (due to phosphate ion) and positively charged protein. The coils can either be condensed or uncondensed (is that a word?). This package is called a nucleosome. Usually, the DNA is only condensed just before replication but is mostly uncondensed for easy access (like an undone fly, y'see). More packaging must take place for a nice & tight package though. The coils coil around into a solenoid shape around a histone 1 core. All these solenoids stack up onto one another which prevents the DNA from getting tangled and heinous. Chromosome: 1 DNA molecule and other packaging proteins etc. Chrmosome pair: 2 homologous chromosomes, one maternal and one paternal. Often similar in characteristics. Chromosome set: total number of chromosomes in a cell. In humans, 46. 22 maternal, 22paternal and 2 sex determining chromosomes, XX or XY. Genome: total genes in a cell. What's a gene? Genes are encoded into the DNA of a cell. Not the whole strand is gene-y goodness. Some bits are genes, other bits are just useless shit. Well, not exactly because you've got all sorts of random stuff there necessary for transcription and translation etc. etc. Genes, like DNA, has a 5' and 3' end (because they're secretly bits of DNA in disguise). They essentially consist of a promoter at the 5' end and a termination area at the 3' end and bunches of alternating exons and introns in the middle. When transcription occurs, the introns get spliced out and the exons spliced together. The promoter is also near a TATA box (where lots of thyamines and ayayayanines are). It's a totally boss box because it lets transcription occur totes m'gotes fast. But how? Well, the lecturer didn't really specify but I'm guessing it's because T's and A's are easily pulled apart because they involve only 2 H-bonds whereas G's and C's involve 3 H-bonds. Fucking pussies. I'm all over the place here... The promoter's also important because that's where RNA polymerase II goes which is an enzyme used to transcribe genes by like... slapping da nucleotides on like a mad dawg. Nucleotides are the functional units found in RNA aswell as DNA and the sugar is ribose instead of deoxyribose as in DNA. Basically, that means that there's a hydroxyl group on the 2' carbon instead of just an oxygen. So, promoters are called control elements because they control shit going down in transcription. You also have transcriptional factors which are proteins which latch onto these regulatory sequences and do all sorts of funky shit. Not sure what but I'm sure they're super important... I think regulatory sequences are just sequences in the DNA that the transcriptional factors recognize and have sex with. Not too sure. Mmm, let's go back to DNA for a second here. DNA replication to be exact. DNA replication is needed when you want to split the cell up in 2 so you need 2 of each chromosome and shit. DNA replication... hmmm... Well, you need to rip apart the DNA all Hulk-style. DNA makes it easier by having a concentration of A's and T's at some point which are easier to de-sex as they only have 2 H-bonds instead of 3. For that, you can use 3 things: DNA gyrase (it gyrates that shit... actually, I think it cuts up a little bit and pulls it apart) or DNA helicase or DNA topoismerase (not sure how to spell that... I'll just write it really smudgily in the exam so no one notices...) which peel apart the strands. So you have this fork now. Two prongs of single strands and then a fragment of the double helix. Now to replicate we need a substrate which is a deoxy-CTP which is just... a nucleotide with 3 phosphates attached? Iunno. So, with ATP you cleave off those dang phosphates and the energy released can be used to glue that shit on the template strand of DNA. So, we need an enzyme called DNA polymerase which... makes polymers of nucleotides. Unfortunately, this shit gets messed up because DNA always has to be made 5' to 3'. Not sure who made up that rule but, whoever they are, they're a fucking asshat. Now we have to remember all this other shit about lagging and leading strands. Leading strands are strands which are made 5' to 3' as per normal. That's because they're made from the prong end and the DNA template strand they have is 3' to 5'. Since they're complementary and all, they're made 5' to 3' so that's all good. But then we have this other dipshit DNA strand that's 5' to 3' just messin' with us. We say to that strand, "Suck my dick." No, really now. Be a bit more mature. We need to haul ass and get all these other enzymes to get their shit together and pitch in with the work. First we need DNA primase which lays down these little fragments of RNA which are complementary to the DNA template strand. So now we have little 3' ends that the DNA polymerase III can attach nucleotides (5' end that is) to. So they do this in this jumbled up fashion, laying bits and pieces here and getting fragments called Okizaki fragments. So we have all these fragments but we want to cut that primer out so we can... this thing called... DNA polymerase I? And that cuts the primer out then we get DNA ligase which... ligases (lol? Is that a word?) all the fragments together and we get a super pretty strand, 5' to 3' like we like and can admire it and stroke it as we should wish. Every DNA fork will thus have one leading strand and one lagging strand. Like a boss. Unfortunately, on the lagging strand you'll end up with it being a bit shorter because you had to remove the primer. Ah! But the body is a wonderland (thanks, John Mayer... even though you broke T-Swift's heart. I'll borrow your lyrics now, castrate you later) and it has this mad enzyme called telomerase which looks like a big chomping machine to me... Anyway, it adds this string of nucleotides, TTAGGG, to the end of the strands of nucleotides so they have this extra bit that can be sacrificed during replication. All good! The bits are called telomeres. But sometimes there can be mistakes! But the DNA polymerase III, as it's bumbling on, stacking on nucleotides like a boss (1000 nt/sec), will notice these lesions as they mess up the structure of the DNA and cut that shit out, fill it up with some sexy new nucleotide and all will be well. Also, you can have homology-dependant repair where the damaged nucleotide is removed and the complementary base on the other strand is used to add in the correct nucleotide. Ah, sweet relief (har har har har har har). Now let's move onto transcription. What's transcription? Transcription is about making them dang RNAs (ribonucleic acid..?). You do this by using the DNA strands as a template for nucleotides which make up the RNA. RNA differs from DNA because it's single stranded and instead of T has U. U is complementary to A. Three main types of RNA are mRNA, tRNA and rRNA. All this is needed in translation (later! Patience, anyone who has read this far... if you have, you have issues and should see a councillor, post haste!). With translation, we need to pull the DNA apart like in replication using gyrase, topoismerase or helicase. We only pull apart a little bit. We're transcribing the genes, you see. So, we pull them apart a bit so we get one coding strand and one non-coding strand. HAR HAR HAR, tricked you! The non-coding strand is actually the one we use also called template strand. The coding strand just hangs around, being a slacker, and is all caulled the sense strand. So, RNA polymerase II binds near the promoter and is in charge of flicking those nucleotides on which are complementary to the template strand. The RNA is made 5' to 3'. The ribonucleotides assemble; they're horny and getting ready for intercourse with the DNA template strand, you see. They're a bit more slack than the DNA polymerase III which can flick on those suckers 1000nt/sec while RNA polymerase II can only do about 30nt/sec because it doesn't have the luxury of fixing up mistakes. As the RNA is made, it's gradually released and the DNA strands come back together all nice. Transcription stops when RNA polymerase II hits the termination signal. We have this immature, naughty, school-aged mRNA now but we need to make it sexy, do it's hair, slap on some face paint, spritz a little eu de smelly on its neck, in the big ol' cleave and behind the knees (God knows why... I mean, knees? Who's smelling the knees? Unless you're some kinky foot fettish person who likes to tease himself with a little knee sniffing first before getting onto the main event...). Right now, we've basically just cause this string of nucleotides based off the template DNA strand (and the gene it had) but it's so raw, like a dead cow. How to make it pretty? Um, by chucking out the introns through this sweet enzyme thingy called a SPLICESOME. Such a dope name. A splicesome consists of snRNP. SMALL NUCLEAR RNA + PROTEINS. And it recognizes these base sequences at the 5' and 3' end of the introns. GU at 5' end and AG at 3' end. The mad dawg splicesome comes along, squeeze the introns into a little lariet (OR HAT) and fucks with it til it clips off and sails away to a better place. Um, also we need to add a 5' hat and a 3' tail to. What for? Well, when translation comes around, the hat and tail are needed for protein binding to initiate translation. Also, when the RNAs are being degraded, the tail is first chopped off and schtuff. And the tail is needed to protect the RNA. The tail is a poly-A tail so I'm guessing it's made of lots of A's... not too sure about that. The cap is a 7methyl-guanine attached to the 5' end by 3 phosphates. Like a boss. To attach these brits and pieces, we need an enzyme called CTD-P. CTD-P also needed to help splicing. Like a boss. Okay, now to translation: that is we are TRANSLATING the DNA language to protein language and making a totally dope protein for use in the cell. To translate the protein we need all sorts of RNA - mRNA, tRNA and rRNA. We have the mRNA which can be divided into groups of 3 bases called codons which code for one amino acid each. There are lots of codons (64, 3 being stop codons which terminate translation) and only a few amino acids so more than one codon codes for each amino acid. Reading frames relate to the frame of codons being reead. Firstly, the mRNA is translocated through pores in the nucleus to wherever it's needed, mayhaps it is chaperoned around by cytoskeleton proteins or what have you. Now, we have this mRNA. But we get the tRNA which is... ummm... RNA-ish except it's all twisty through H-bonds and what have you and it has this thing called an anticodon, a specific sequence of bases which will be complementary to a part of the mRNA so it can latch on and do it's business. That is to say, ejaculate some amino acids on it. An amino acid binds onto the tRNA at the side opposite to the anticodon which is directed by an enzyme called AA-tRNA synthetase. Now, with the AA, it makes an aminoacyl-tRNA. Hmm... that makes sense. Amino acyl. Amino acid. tRNA. tRNA. GOOD GOD. REVOLUTIONARY STUFF. We've got this fat ass aminoacyl-tRNA now and it's hopping along. The carboxyl terminus of the amio acid is attached to the tRNA so in the end we'll have the amino terminus attached to the mRNA before it hops off and goes on its merry way. What's rRNA? Vell, ribosomes are made in the nucleolus and are where proteins are protein-sethysed. They're made up of two subunits; one large one small, comprimsed of rRNA and other proteins etc. etc. They join up to help synthesise proteins when the actual tRNA bumbles along, all aminoacyl etc. Initiation occurs when everything comes together and the first tRNA lands with its met amino acid attached. Met is always the first amino acid. It goes to the P-site. The next tRNA comes to the A-site and the met hops on. The reading frame shifts and the process continues with each used tRNA being released. The ribosome catalyses the formation of peptide bonds between amino acids. When a termination signal (STOP CODON) is reached elongation STOPS and everything floats away, airy fairy. Lots of ribosomes can work on the same RNA at the same time to make lots of proteins, all similar. Now the polypeptide is released to do its magic around the cell. As for controlling gene expression and RNA function. Firstly, let's review the gene. We have this super dope gene, all genie and functiony. Transcriptional control is the main form of control of gene expression. If the gene doesn't need to be transcribed into mRNA, it stop right there.Cis-acting control elements regulate transcription and are found on the same chromosome while trans-acting elements can be off in the clouds, doing their business elsewhere. To summise (LOL SUMMISE! SUMMARISE! LOL! SUMMISE! THEY'RE LIKE THE SAME WORD LOLOLOL), transcriptional control involves the promoter at 5' region of gene, termination signal (STOP CODON) at 3' end and these elements for regulating shit, either on gene or elsewhere. We also have other elements like enhancers or repressors which enhance and repress transcription of a gene. Often these elements are tissue specific and only function in differentiated cells. Really, the promoter is probably the most important one as it initiates transcription and is where the RNA polymerase II lands. Also, the TATA box which is... somewhere near the promoter? Lots of T's and A's for rapid transcription. Transcription factors are proteins which bind onto the gene after external stimuli like hormones. Can be general (house-keeping) or tissue specific for particular functions. Transcription factors are super important for transcription and bind to particular sequences in the gene so mutations can fuck that shit up and screw up transcription. These sequences are called regulatory sequences. Now, back to the TATA box (boss) which is about 25 base pairs away from the promoter. Some transcription factors bind to it as part of the general transcription factors. This causes kinkage in the RNA. This initial binding recruits all the other transcription factors. After this, RNA polymerase II can jump on the bandwagon on transcribe away. Let's review the 5' cap and 3' poly-A tail. The tail is to protect the mRNA, to be chopped off when degraded and so proteins can bind to it to initiate transcription. The cap is made of 7methyl-guanine attached by 3 phosphates to the 5' end and the tail is made of ribonucleotides with adenine base. It is added by separate enzymes while CTD-P is necessary for adding both the cap and tail. Oh shoot, think I got something wrong. CAP is for PROTECTING the dang RNA from degradation and also for proteins to attach to initiate translation. TAIL is chopped off at degradation and also for proteins to attach. As for translational control... Normal development requires coupling between translational control and location so the right protein is made in right place. Especially important for embryos because they're special and stuff. The RNA needs a cap and tail for proteins to initiate to start translation too. To degradation now. RNAs have half lives which can last for a few hours or less than 30 minutes. Proteins catalyse tail shortening (compete with translational proteins which also use them for initiation of translation). The degradation of the poly-A tail increases degradation especially when it reaches 30 nucleotides. Loss of poly-A tail leads to loss of message. Cap can be killed too which speeds up degradation. Another type of RNA is RNAi or RNA interference which is a natural mechanism to protect cell from DNA. RNAi is a double helix RNA. It gets diced up into fragments called small interfering RNA (siRNA). Fragments bind to RISC (RNA induced silencing complex). Guide RNAs guide complementary mRNA there to be decimated. MicroRNAs similar and cause degradation. Short, 25-30 nucleotides.

FUCK. THIS IS SHIT.

J