Transcription

DNA to RNA to Protein

The central dogma of molecular biology states that DNA leads to RNA and then leads to proteinsLarge molecules made of amino acids with various functions in the body..  What does this mean, though?  Your cellsThe basic structural and functional units of life. carry chromosomes that are made of DNA.  But, the DNA only holds the instructions for making a protein.  That’s all, just info storage.  There is a process called protein synthesis in which the DNA is accessed for its instructions and then the instructions are used to build a protein.  So that explains the blue DNA on the picture and the purple amino acidThe building blocks of proteins, consisting of an amino group, carboxyl group, and side chain. chain, but what’s the pink?  In this process, an intermediary is used to carry the information from the nucleusThe control center of the cell that contains DNA and directs cellular activities. in the DNA to the place in the cytoplasmThe gel-like substance within a cell that contains organelles and cytosol. where the protein will be assembled according to the instructions in the DNA.

All right, so, I have a Swedish lineage and I have my great-great-grandmother’s cookbook.  It’s in Swedish.  I needed it translated, and doing it myself was quite slow going.  I found a woman on the internet that did translationThe process of converting mRNA into a protein. services for Swedish to English.  She was on the west coast, but I didn’t care where she was because I was NOT sending her my great-great-grandmother’s cookbook.  I made a copy, send her the copy, she translated it, and sent me back the English version.  I then made wonderful Swedish recipes like curried egg salad and salted cod.  Yeah, great.  But, the point is that I retained the original, like the DNA stays in the nucleus.  And I sent out a copy to be translated into this new language, just as RNA, the pink on the diagram, carries the instructions for making the protein to be translated from nucleic acidA substance that releases hydrogen ions (H⁺) in solution. to amino acids. 

What does this all mean for you?  Your DNA holds the instructions for the proteins that make you you.  For example, there are pigmentation genes in your chromosomes, they carry instructions for making a pigment of a certain color, and that pigment can be made and then inserted into your eyes to be expressed for the word to see.

Protein Synthesis

Taking the instructions in DNA and making it into RNA and then into an amino acid sequence is a two part process.  First, we have to make a disposable copy of the DNA that can travel out of the nucleus and get destroyed and we don’t care.  This is like me making the copy of the cook book.  This is called transcription.  This word just means “to copy.”  This is what you do when you copy someone’s notes if you miss class; you transcribe their notes.  More specifically, we are going to make something called mRNA, m for messenger.  This is the disposable copy that is produced in transcription.  This is what is taking place in the top part of this picture, in the nucleus of the cell.  On the next slide, you will see a close up of that part of the DNA double helixThe twisted-ladder structure of DNA molecules. that is just slightly unwound.  That is where the copying is taking place. There is an enzyme called DNA helicaseAn enzyme that unwinds and separates DNA strands during replication. that gets in there and breaks the hydrogen bondsWeak attractions between hydrogen and electronegative atoms like oxygen or nitrogen. between the nitrogenous bases of the nucleotidesThe building blocks of nucleic acids..  This bond breakage allows the DNA to unwind.  This is a lot like DNA replication, up to this point.  But instead of using the enzyme DNA polymeraseAn enzyme that synthesizes new DNA strands by adding nucleotides to a template., an enzyme named RNA polymeraseAn enzyme that synthesizes RNA from a DNA template. inserts itself into the DNA bubble.  It’s this enzyme that will make the mRNA.

Transcription

This is a picture of transcription.   That big blob there is not the nucleus, although we are going to assume that this process we see here is taking place in the nucleus.   The big blob is an enzyme called RNA polymerase.  Just like DNA polymerase, RNA polymerase makes the RNA polymer.  It knows the base pairingThe specific hydrogen bonding between complementary bases (A-T, C-G in DNA). rules too, but it thinks that adenineA purine nitrogenous base found in DNA and RNA, pairs with thymine (DNA) or uracil (RNA). will always connect with uracil whereas DNA polymerase things that adenine and thymine always pair up. Unlike DNA replication that wants to copy the entire length of DNA that makes up one of those long pieces of DNA called a chromosome, transcription targets only certain areas on the DNA.  These areas are genes.  They contain sequences of nucleotides that hold the recipe for making one protein – or at, least, that is what we are going to leave it at right now.  When we unwind the DNA, we have the two strands of DNA, but we aren’t going to take the sequence from both of them, just one.  The strand holding the gene sequence is called the template or coding strand.  This is the blue strand on the bottom of the picture.  The top strand is called the non-coding or non-template strand and just kinda hangs out.  But, notice that if you know the sequence of a non-coding strand, you could use the baseA substance that accepts hydrogen ions (H⁺) or releases hydroxide ions (OH⁻). pairing rules for DNA to determine the sequence of the coding strand. 

OK, so RNA polymerase gets in there and starts reading the DNA from the 3’ end headed toward the 5’ end of the coding sequence, or the specific strip of DNA holding the gene in question. RNA polymerase does the same thing that DNA polymerase does, with one small difference.  RNA polymerase encounters a guanine and yells out for the match – cytosineA pyrimidine nitrogenous base that pairs with guanine in DNA and RNA..  It does the opposite when it encounters a cytosine by yelling out for a guanine.  When it encounter a thymine, it yells out for an adenine, but when it encounters an adenine, it calls out for uracil.  This is because RNA polymerase knows the base pairing rules for RNA.  In the picture in this slide, the red nucleotides are being brought over to pair with the DNA nucleotides making a transcript.  This transcript is disposable.  What do I care?  I still have my DNA and can access it again if I need to.

RNA transcripts can be long, like one long word.  But it’s not, it is many three-letter words.  We will find out later why this is the case, but we call a sequence of three nucleotides on mRNA codons.  So, in the picture on this slide, CAU would be the first codon on the mRNA.  It would also be the codon at the 5’ end of RNA.  CCA would be the second codon as we move toward the 5 ‘ end and AUU would be the third codon.  It’s important to remember that codons are on the mRNA. 

genes that make insulin, stopping its production.

Transcription
Factors

Transcription is actually much more complicated than this.  How does RNA polymerase know where to attach?  How does it know when to detach? 

For example, gray hairs.  Gray hairs are the result of a gene that starts to become transcribed.  It’s a gene you always had, but it’s been turned on like a light bulb.  You didn’t always make the proteins that made that white pigment, but some stressful event in your life turned it on.  This could be an emotionally stressful event a traumatic event, or this could also be a physically stressful event such as a surgery or childbirth.  What happens is that there are these little proteins called transcription factors that can either initiate transcription or prevent transcription.  In our analogy of gray hairs, maybe a negative transcription factor or a repressor that prevents transcription is removed by the stressful event or maybe a positive transcription factor called an activator that initiates transcription is added.  Either way, transcription starts. 

There are many hormones that the human body makes that are called antagonistic hormones.  Most of these are peptide hormones derived from proteins.  Insulin, the glucoseA simple sugar that is the main source of energy for cells. lowering hormone and glucagonIncreases blood sugar by promoting glycogen breakdown., the blood glucose raising hormone fall into this category.  When your blood glucose goes above a certain level, the cells in your pancreasA gland that produces digestive enzymes and hormones like insulin and glucagon. make insulin.  When your blood glucose goes below a certain level, the cells in your pancreas make glucagon.  Put another way, when your blood glucose goes up, positive transcription factors are put onto your genes that make insulin and insulin is made.  When your blood glucose goes down negative transcription factors are put onto the genes that make insulin, stopping its production.

mRNA Degradation

So, at the end of transcription, we have a disposable mRNA transcript that leaves the nucleus goes into the cytoplasm and seeks out a ribosome to start translation.  Right now in the cells of your pancreas, this is happening so that you can make some enzymesProteins that speed up chemical reactions in the body. for digestion.  In the cytoplasm of your pancreatic cells there are tons of mRNA transcripts floating around, looking for a ribosome.  Some of these will become degraded before they can connect with a ribosome.  The activity of the enzymes that can degrade the transcripts is just one way in which you could have the gene, but never make the protein.  It is possible that even though you are transcribing mRNA transcripts, they are degraded before they can be translated.  This is just one way in which someone could be lactoseA disaccharide sugar found in milk. intolerant.  Some people don’t even have the genetic codeThe set of rules by which DNA sequences are translated into proteins. for the lactase enzyme and transcription doesn’t ever occur.  Some people have the genetic code, but have overactive enzymes that degreade the transcript before the protein can be made.  This is the difference of genetic lactose intolerance or environmental lactose intolerance, which can occur from the long-term use of antibiotics such as tetracycline.  Lyme’s disease is treating with a long course of tetracycline-like antibiotics giving patient’s a choice: Lyme’s Disease of lactose intolerance.  Which do you want because you can’t have your cake and eat it to.  All medications come with a trade-off.  

mRNA processing

The enzymes in your cells are always looking the catabolize or breakdown nucleic acids.  These enzymes are like Pac Men for DNA and RNA.  Strange, right?  No.  That’s why DNA is trapped in your nucleus.  Also, you are basically just a recycling center.  You eat the DNA of other organisms and break down their DNA and use the components to build back up your own.  Your cells are always digesting DNA. 

In order to protect the mRNA we put a helmet and steel toed boots on it before we send it out into the cytoplasm.  This is a process called mRNA processing and it does more than just the helmet and boots.  The helmet and boots are technically called a cap and tail (although I still think helmet and boots is better…and funnier). This cap and tail are made of just a bunch of repetitive nucleotides, like a long chain of adenines added at the end.  This way, if any of those enzymes actually start to eat into the DNA, no valuable parts of that coding sequence will be lost.  We can sacrifice the cap and tail and still make our protein.

The other things that happens in mRNA processing is something called slicing.  So, I kinda lied when I said one gene holds the recipe for one proteins.  That’s not true because splicing can give us a bunch of mini-sequences.  mRNA has lengths of sequences called introns and exons.  In a process called splicing, introns are removed from the transcript and exons are left over, glued together, and now form a mini-sequence derived from the originally transcribed sequence.  This. Is. Genius.  This is how so many variations of protein recipes can be held by one gene.  With differential splicing, the possibilities of sequences are endless.  Well, maybe not endless, there’s probably some mathematical equation with an exponent involved that tells us how to calculate that.