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The chemistry of DNA replications leaves linear chromosomes getting shorter with each round of replication. Read More...

DNA Replication 1

DNA Replication

Let me lay out the basics:
Since DNA is two complimentary strands, each strand contains the information to specify the other. Thus, it seemed logical from the first time the structure was determined that the two strands would separate and new subunits (deoxyribonucleotides) would be added to make each new strand, using the other old strand as a template. Each new double helix would therefore really be one old strand and one new one.
Here is the basic idea in video. Like most of the videos I will link, these come from the Howard Hughes Medical Institutes (HHMI). Note that this video shows the new strands being made the same for both templates. As we know (and the video alludes), this cannot happen.

The first problem:

So, one strand is the template for the other. New bases are added one at a time via a simple chemical reaction we have talked about, mediated by a complicated enzyme machine (comprising many different proteins).
The problem is that the chemistry requires that a new subunit can only be added to the 3’ end. So, if you are moving along a replication fork, one strand cannot be replicated easily…the fork is moving the wrong way and it has to be replicated “backward.”
Here’s a more basic video that shows you how an Origin of replication might work and some detail, but in a much simpler form.
Here are two other videos
here and here that have merit, though all of them, including the cool one below, have errors in them.

Notice that there is a second problem.
As the video says, you need a short RNA primer to begin each section when synthesizing the lagging strand. This is put down by an enzyme called “primase.” The leading strand needed an RNA primer to get started too. But, since it is replicated continuously, it only needs one primer, way back at the start of replication.
Here is a link to the really cool video. I think you should look at it again, now that you have seen the simple one. We have to name all the enzymes and talk more about details tomorrow.

Here are the details of the problem

The unit of DNA polymerization (Synthesis) is a deoxyribonucleoside triphosphate. In the image, the “Base” would be either A, T, C or G, depending on what was on the template strand. Just like ATP, these molecules have high-energy (unstable, that is) bonds joining the phosphates. This can therefore be used in transfer reactions, just like enzymes transfer phosphates from ATP in reactions we have studied. There is a seemingly subtle change: instead of the third (
𝛄 or “gamma”) phosphate on the end being attacked by the OH on the 3' carbon, the first one is (called “α”). This change has a big impact, though. It links the 3' carbon of the existing DNA to the 5' carbon of the incoming base via a phosphate.
This is called a “phosphodiester.”

Here is a specific example, deoxyATP
The next base that comes in will use the high-energy triphosphate it carries to attack the 3' OH.
And forms this:

Thus, as we said, we must add DNA to the growing 3' end. From a chemical standpoint, there isn’t any reason why you cannot add an incoming base to the 5' end, provided that end has a 5' triphosphate. That triphosphate would be unstable, however. Should it hydrolyze, the new DNA wouldn’t be made until another enzyme came in and “recharged it” with new phosphates.

Intro Translation

Key Words

Ribosome: the machine that synthesizes protein by translating the code of the mRNA (with the aid of tRNA). It has a small and large subunit and is made mainly of RNA.
  1. tRNA: Transfer RNA is the adaptor molecule that ferries the amino acid to the ribosome. It has an anticodon; a three-base sequence that reads the codon.
  2. Codon: three-base sequence on the mRNA that encodes an amino acid
  3. Anticodon: three-base sequence on the tRNA that reads the codon. It is complimentary to it.
  4. “A-site”: Anterior (or "Amino-acyl) site on the ribosome. This is the site where the tRNA enters with the amino acid linked to it's 3' CCA sequence.
  5. “P-site”: Posterior site (or "peptidyl" site). This is the site in the ribosome where the tRNA with the growing protein chain is attached.
  6. “E-site”: exit site on the ribosome.
  7. Start Codon: the initiator tRNA, which holds the first amino acid reads the codon AUG and carries the amino acid Methionine (Met, or “M”). The anticodon for the start codon is 5'CAU (think about).
  8. Stop Codon: there are three codons that tell the ribosome to stop translation (UAG; UAA, UGA).
  9. Reading Frame: Since the code is read in groups of three, non-overlapping bases, Any stretch of mRNA has three possible reading frames. Only one reading frame at a time is used.
  10. ORF, or Open Reading Frame: A stretch of codons that starts with an AUG and ends with a stop codon and therefore can encode a protein. While I usually only write out a few, a typical ORF would encode hundreds of amino acids. Collagen, for example, is a large protein and is 1400 amino acids or so long.


I’m going to draw a bit on wikipedia for this. Here is a figure from them:

Translation Overview
And here is a link to the video from HHMI. Translation in eukaryotes proceeds at about two amino acids per second. Bacteria is closer to 20 AA/second.

Regulatory sequences

Recall that there is a 5' untranslated sequence on the mRNA. There you will find sequences that direct the ribosome to the start of the protein-coding sequence. In bacteria, that sequence is more important and well characterized. In Eukaryotes, the regulation of where to start is less well understood…but we are learning.
This sets the reading frame:
Consider the sequence of letters BATHECATWASBADTHEDAYSHEBITTHEDOGOT, you can find the meaning only by starting at the correct letter (In this case, the third letter: THE CAT WAS BAD THE DAY SHE BIT THE DOG). If you start with BAT…that works…but the rest is not meaningful: HEC ATW ASB ADO).
The AUG tells the ribosome: put a Methionine here and keep reading in this frame. After some long series of amino acids, the Ribosome will encounter a stop codon, and release the mRNA (which does require a protein "released factor") and the newly made protein. Multiple ribosomes can be reading a single mRNA at one time, lined up one after the other.
The Code:
You need a triplet codon because you need three nucleotides to get enough possible combinations to encode all 20 Amino acids (there are 64 possible combinations, three of them are stop codons). The rest of the code is given below. Note that most amino acids have more than one codon. We say the code is “degenerate,” for this reason.
Here is the general code. Note that not every organism uses exactly this code. In a couple of organisms, UGA is read as a tryptophan codon, for example. How would this happen? Take a look at the where Tryptophan is in the codon table and predict what could change to lead to UGA becoming a stop codon.


More detail on the mechanism:

Of course, there is more…much more. Here is a really cool video (with an interesting sound track) from a lab that works on one of my favorite proteins: EF-Tu (elongation factor Tu is the name for the protein in bacteria. But, the function exists in eukaryotic systems also).
EF-Tu is arguably the original G-protein (certainly the first one we figured out). It sets the minimum time a tRNA must stay in the ribosome before the peptide bond is formed. In this way, accuracy is greatly improved.
Also, while there is some argument on the details, the GTP hydrolysis is thought to be part of what drives the assembly to "ratchet" to the next site.

The next video up should be this one:

it's good too.

The Operon


An operon is a system that exists in bacteria, but not in eukaryotes, for regulating several genes together. Suppose, for example, you are a bacteria that sometimes encounters the sugar lactose. It would be good to have the genes for proteins to process that. You’d need a transport protein, and an enzyme to break the lactose into its components, Glucose and Galactose (which you can also convert to glucose).
But, you wouldn’t want to be making these proteins all the time. It would be a waste of energy. Ideally, you would have a system that kept the genes for these proteins “Off,” but then be able to sense the presence of lactose and turn the genes “On.”
That is the
lac operon. And it serves as an example.

What an operon needs

  1. A stretch of DNA that encodes several proteins on ONE mRNA. The ribosome will make all of them reading the same message. This does not happen in Eukaryotes.
  2. Promoter: a site on the DNA recognized by RNA polymerase (which carries its own transcription factor to bind the promoter sequence, in E. coli).
  3. Operator: A sequence in the DNA that binds another protein, called Repressor. When repressor is bound, the polymerase cannot get access to the promoter.
  4. A Repressor: The protein that binds the Operator and prevents transcription. It is usually encoded nearby, transcribed from another promoter. Importantly, the repressor has to exist in two states: One that binds the operator and prevents transcription of the genes and one that does not.
  5. Effector molecule: molecule, such as lactose in the example of the lac operon, that binds to repressor and switches it between the two states.

Below is a general picture taken from Wikipedia.
The players are numbered below as:
  1. RNA Polymerase
  2. Repressor
  3. Promoter
  4. Operator
  5. Inducer (such as Lactose)
  6. 6, 7 and 8: the coding sequences for several proteins.
In the first panel, the repressor is bound because the inducer is absent. RNA polymerase cannot gain access to the gene.
In the second panel, the inducer changes the shape of the repressor, which causes it to release from the operator. Transcription can then occur.
Note, that there are also cases where the repressor binds only in the presence of the effector molecule. So, you can turn off an operon when the effector is present. This is great for feedback inhibition. The Trp operon is an example of this and is described in the book.