Quiz 3 Review Answers
Supplemental Instruction
IowaStateUniversity / Leader: / Matt C.
Course: / Biol/Gen 313
Instructor: / Dr. Rodermel
Date: / 09/24/2017

Introduction: This review sheet will cover the cell cycle and DNA replication. Chapters 2 and 10 examine these topics.

Material

  1. What is the purpose of interphase?

Interphase allows the cell to grow, reproduce its DNA, interact with other cells, and perform specialized functions in multicellular organisms.

  1. What are the cell cycle checkpoints for?

The cell cycle checkpoints ensure that the cell can continue on to subsequent steps in the cycle without errors. The early checkpoints check for sufficient cellular growth, signals from other cells and a lack of DNA damage. The G2 checkpoint ensures that the genome was copied. The M-phase checkpoint checks alignment of the chromosomes and connection of the spindle fibers.

Without the checkpoints, genomes would be highly variable in daughter cells with many large-scale mutations occurring.

  1. Diagram out a mitotic cell cycle for a cell with two chromosomes.

Like this, but with two chromosomes instead of six. Each X is a chromosome from prophase to metaphase, while each linear molecule is a chromosome everywhere else.

  1. What does licensing help with in eukaryotes?

Licensing helps eukaryotes avoid over-replicating their DNA. The replication cycle is much more particular in eukaryotes and having more than exactly two copies of any chromosome can have a dramatic effect on phenotype. Licensing marks the eukaryotic origins of replication so that they are only replicated once.

  1. How does licensing differ in prokaryotes?

An annoying Matt question. Prokaryotes don’t use licensing. They just replicate all the time.

  1. There are 9 proteins / protein complexes to remember for prokaryotic replication. In the table below, write each of their names, their functions, and their analog in eukaryotes.

Protein / Function / Eukaryotic Analog
Initiator proteins / Recognize the prokaryotic origin of replication (ori site) and begin to unwind the DNA – forms a bubble. / Origin Recognition Complex (ORC) – Different in that it has to recognize many more origin sequences than the prokaryotic initiator proteins.
DnaB – DNA helicase / Unwinds double-stranded DNA at the replication fork. / Helicases – there are several helicases used in eukaryotes.
DNA Gyrase / Releases supercoiling caused by DnaB, allowing DnaB to keep going. / Topoisomerases – eukaryotes use the general name for gyrase and, again, have several.
Single-stranded binding protein (SSB) / Keeps ssDNA from coming back together or forming other secondary structures. / RPA – a protein that also binds ssDNA, but is not SSB. Really, just a different name.
Primase / Creates RNA primers that offer a free 3’ – OH to be used by DNA polymerases. Is an RNA polymerase / Polymerase α – Also creates RNA primers, but does have DNA polymerase activity. A low-fidelity DNA polymerase
Polymerase III / Synthesizes DNA. Has proofreading (3’-5’ exonuclease) activity. / Polymerases δ and ε – This job appears to be split in eukaryotes, with ε synthesizing the leading strand and δ the lagging. Both are also high-fidelity.
Polymerase I / Removes (5’-3’ exonuclease) and replaces the RNA primers. / Polymerase δ – kind of. Pol δ doesn’t have the 5’-3’ exonuclease activity, but a different protein does that for Pol δ. Pol δ does replace the primer, though.
Ligase / Attaches fragments together. / Also DNA ligase.
Tus / Involved in termination. Blocks DnaB from continuing to move. / Not a problem in eukaryotes except when replicating chloroplasts or mitochondria, in which case they use bacterial systems.
  1. What does fidelity mean in regards to replication?

How well the polymerase matches the template strand when making new DNA. A high-fidelity polymerase doesn’t make mistakes very often while a low-fidelity polymerase screws up frequently. Pol δ and Pol ε are high-fidelity while Pol α is low-fidelity.

  1. What does camptothecin do?

This is the active ingredient from the plant that Dr. Rodermel showed in class. A version of it is used in cancer treatment. Camptothecin inhibits topoisomerase activity, preventing the replication fork from expanding and thereby preventing cell replication.

  1. What is the end-replication problem?

Eukaryotes have linear chromosomes, so every time they replicate there are regions on the end of each side that go un-replicated because Pol α doesn’t have enough DNA to grab onto. These are the 3’ overhangs. Since the primer can’t be set, no Okazaki fragment is made and there is a strand of ssDNA left. Nucleases in the nucleus would then chop up the ssDNA and the eukaryotes chromosomes would get shorter and shorter until it died.

  1. How does telomerase work?

Telomerase is actually a reverse transcriptase – it makes DNA from an RNA template. Specifically, the RNA template that it keeps inside of itself since telomerase is a ribonucleoprotein. The RNA in telomerase is a repeating pattern with lots of Cs. It binds to the consensus sequence for a telomere at the end of the 3’ overhang with one repeat of the pattern sticking to the DNA and the others hanging off. Telomerase then synthesizes new DNA onto the overhang using the RNA as a template. This creates new, G-rich DNA. Telomerase does this several more times until there is enough of an overhang that Pol α can finally make a primer. In the end, there will still be an overhang that gets chewed off, but since the dsDNA has surpassed its previous length, the chromosome won’t shorten.