Homologous Recombination (HR) When replication fails catastrophically due to a lesion on the leading-strand template , the DNA being copied — the leading nascent strand — can break or become chewed back, leaving its 3′ end--the end that DNA polymerase epsilon needs to restart--located behind the polymerase, where it is inaccessible to the polymerase. If the fork simply tries to resume, it can’t: there is no usable 3' end starting point. At this point, the fork reverses, and

In the last post, we talked about fork protection , a posture that replication forks take when a lesion stalls a polymerase. Fork protection unfolds in minutes to tens of minutes after the cell detects RPA-dsDNA. Recall that it stabilizes the replisome structure and protects exposed DNA, giving the cell time to deal with the lesion. But fork protection is only the first part of a two-part process called fork stabilization . Fork stabilization also includes fork reversal. How

In the last post, I introduced the cell's two main DNA lesion repair pathways-- base excision repair (BER) and nucleotide excision repair (NER) . Both operate well beyond the replication fork during all of the phases of the cell cycle. But what happens if a lesion escapes BER and NER and finds itself in S phase in front of a moving replication fork? Most DNA lesions get past the CMG helicase but not the DNA polymerase, although some very large lesions can't get past the heli

In addition to DNA polymerase errors, the human genome--even in a perfectly healthy cell--is under constant assault from endogenous  (internal to the cell) and exogenous  (external to the cell, or environmental) chemicals and other agents that alter its chemistry, break its backbone, and distort its helical structure. In this post, we'll first consider what lesions are. We'll see that some are modest (e.g., a small chemical change to the base on a nucleotide) and some are mo

As I mentioned in the last post, DNA polymerases sometimes insert a ribonucleotide (an RNA monomer) into a growing chain instead of a deoxyribonucleotide (a DNA monomer). When that happens, the bases do pair correctly. But the extra small chemical group that differentiates a deoxyribonucleotide from a ribonucleotides can still causes problems like strand breakage. DNA vs RNA . The sugar portion in a ribonucleotide is a ribose whereas in a deoxyribonucleotide it is a deoxyribo

Life can't exist without the high fidelity transmission of genetic information from parent cell to daughter cell. DNA polymerases plays the central role in accomplishing this. DNA polymerases delta and epsilon only make an error (that is, attach a non-complementary nucleotide to a growing chain) once every 100,000 to 1 million nucleotide additions. But this is still too many. Those that arise must be fixed via a back-up system. In addition to polymerase errors, the human ge

As the CMG helicase moves along the double helix separating it into a leading and a lagging strand, it creates what is often referred to...

DNA polymerases can only synthesize DNA in the 5' to 3' direction. That is an absolute rule that's determined by the biochemistry of nucleotide addition. Given the antiparallel nature of DNA, a corollary is that DNA polymerases can only synthesize off template DNA that is oppositely oriented in the 3' to 5' direction. Our leading strand exited the MCM2-7 ring of the CMG helicase 3' end first. So the DNA strand that will be synthesized using that strand as a template will be s

An important fact: The two DNA strands in a double helix are oriented in an antiparallel manner. That is, they run in opposite directions like the lanes of a two-lane highway. Recalling chapter ___, scientists describe the orientation of a given single strand of DNA as running either “3’-to-5’” (three prime to five prime) or “5’-to-3’” (five prime to three prime) based on the orientations of the deoxyribose sugars in the DNA backbone. But as a hard and fast rule, DNA polymera

Let's take a closer look at two amazing molecular machines found in the replisome: the CMG helicase and the PCNA sliding clamp . Both...

Our cell of interest is now in S phase and 30,000-50,000 replication origins along its genome have become licensed. The replication origins are licensed based on the presence of two MCM2-7 protein complexes (the licensing factors) lined up head-to-head forming a MCM double hexamer, or MCM-DH. Assembling a functioning replisome starting from an MCM-DH at a replication origin will involve the following four steps: (1) transformation of each of the MCM2-7s into a complete (but s

As we kick off the focus of this book—a deep dive into human genome replication—we’ll see that the process involves many different...

If someone had wanted a book in the 15th century it would have had to have been copied by hand from an existing one. The scribe would...

In this post I present a perfect example of ATP-driven protein motor movement. ATP is a frequently employed driver of protein movement in...

Each time a cell divides, it creates a copy of both its genomes for the two daughter cells. It does so with extremely high accuracy (or "fidelity" in molecular biology parlance). Human cells copy their genomes with 99.99999999% accuracy. That equates to one single error per every 100 million nucleotides! Stop and think about that! In this post, we're going to review eight reasons why replicating the human genome is so challenging. Of course, the cell overcomes these challen

A cell is a dynamic place. Enzymes are speeding up chemical reactions. DNA, RNA, and proteins are being synthesized. Molecular motors are...

Two human genomes adding up to 6 billion base pairs are contained in the nucleus of every cell in your body. Different kinds of cells use...

We've covered proteins : polymers of amino acid monomers that fold up and perform most of the tasks in the cell. We've also covered DNA...

My last post covered the structure of DNA: what DNA is. In this post, I move on to function: what DNA does, or, maybe better, how DNA...

In this "Part I" post I'll be focusing on the structure of DNA--what DNA is . In the next, I'll cover how DNA functions--what it does ....