DNA Replication Concepts

• Meselson-Stahl experiment results supporting the semiconservative model over the dispersive model include the following

• In the first generation after transfer from 15N to 14N medium, DNA is of intermediate density

• In the first generation after transfer from 15N to 14N medium, DNA after denaturation is half heavy density and half light density

• False statements regarding DNA synthesis:

• DNA polymerase cleaves two phosphates from the 3' end of the newly added deoxyribonucleotide as it is added during DNA synthesis

• If base pairing is incorrect after adding a deoxyribonucleotide, the polymerase typically cleaves the phosphodiester bond and repeats the addition

• Strand C in the image is the lagging strand

• The DNA polymerase initiating Okazaki fragment synthesis uses an RNA molecule as a primer

• During proofreading by DNA polymerase, a mismatched deoxyribonucleotide base is removed after being added to the newly synthesized strand and it is removed from the 3' end of the newly synthesized strand

• DNA polymerase does not require a primer to begin synthesis

• Telomerase does not require a primer to begin synthesis

• Arrow A points to the sliding clamp

• Telomerase adds DNA to the lagging strand template at chromosome ends

• Telomerase uses RNA as a template for synthesizing complementary DNA in the lagging strand template

• Deamination is a DNA damage event involving conversion of cytosine to uracil

• An enzyme that recognizes the damaged base and excises part of the other strand is NOT involved in repair mechanism

• The function of this enzyme is to complement the damaged strand

• In homologous recombination, the DNA in the unbroken chromosome, complementary to the invading 3' end of the broken chromosome is what provides the initial template for resynthesis of DNA

• Cholesterol does not include a glycerol molecule with fatty acids attached

• Constant movement of membrane lipid molecules from one layer of the lipid bilayer to the other layer of the lipid bilayer is NOT produced by the self-organizing properties of amphipathic membrane phospholipids

• To maintain constant fluidity when increasing a bacterium's temperature from 20°C to 30°C, the organism might increase the number of saturated fatty acid tails in its membrane or increase the length of the fatty acid tails in its membrane

• Lipids extensively modified with sugars in the Golgi apparatus are not typically moved to the cytosolic side by flippases

• Flippases hydrolyze ATP for selective lipid transfer from the exterior (lumenal) side of the Golgi membrane to the cytosolic side

• The protein part outside the Golgi, shown as "membrane glycoprotein," would end up on the cytosolic side of the vesicle that is forming and the cytosolic side of the plasma membrane.

• A beta barrel sheet pore transferring hydrophilic substances across a membrane would have hydrophobic residues facing the membrane and hydrophilic residues facing the inside of the barrel

• A peripheral membrane protein is most likely extracted by increasing salt concentration

• Detergent molecules usually contain more than one long fatty acid tail

• A non-tethered protein in Fluorescence Recovery After Photo-bleaching (FRAP) produces rapid fluorescence recovery after photo-bleaching

• The intermediate filament dimer is the largest assembly unit of an intermediate filament that has polarity

• Intermediate filaments connect indirectly to neighboring cells via desmosomes, creating a continuous mechanical link

• Plectin is an accessory protein connecting intermediate filaments to other cytoskeletal filaments

• Alpha tubulin is typically exposed at the negative end of a growing microtubule

• Microtubules disassemble in "catastrophe" events at the positive end with tubulin dimers bound to GDP

• Microtubules continue to grow until all free tubulin subunits are used up in a solution with microtubules, unassembled tubulin heterodimers, and a non-hydrolyzable GTP analog

• Microtubules move in the direction of their plus ends when dynein molecules are attached to a glass slide

• The linker protein converts sliding to bending in cilium movement

• Actin filaments are assembled from a single type of monomer that all point in the same direction in a single strand, and filaments are formed from helices of two strands

• In vivo, actin filaments typically assemble as ATP-bound actin adds to the positive end and disassembles as ADP-bound actin is removed from the negative end

• Actin-related proteins (ARPs) can cause actin filaments to form branch points

• In the myosin cycle on actin, myosin releases when binding to unhydrolyzed ATP

• Z discs move closer together during skeletal muscle contraction

• Tropomyosin movement on actin filaments exposes myosin-binding sites in response to calcium binding.

• The correct order of the cell cycle phases is S, G2, M, G1

• A cell decides to initiate the cell cycle at the G1 START checkpoint when the environment is favorable for division

• The Cdc25 phosphatase activates Cdk kinase activity

• Ubiquitylation and degradation of cyclin stops the activity of a cyclin-dependent kinase (Cdk)

• Phosphorylated Retinoblastoma protein (Rb) releases a transcription factor to facilitate cell cycle progression

• Prometaphase is the phase of mitosis when the nuclear membrane breaks down and microtubules attach to chromosomes

• Cdc25 phosphatase is activated quickly by M-Cdk, which then dephosphorylates an inhibitory site in other M-Cdk molecules

• Centrosomes duplicate during the S/G2 phases, nucleate nonkinetochore microtubules, nucleate kinetochore microtubules, and nucleate aster microtubules

• M-cyclin and cohesins are degraded by the Anaphase Promoting Complex (APC) during mitosis

• Caspases activate when their peptide bonds are cleaved

• Degradation of the apoptosome and binding of the degradation products to an initiator caspase is NOT part of an apoptosis-inducing pathway

• Cell survival is promoted when transcription of the Bcl2 gene increases and the activities of Bax and Bak are inhibited

• Myostatin inhibits the growth and proliferation of muscle cell precursors and leads to enhanced muscle production in mutants without its function

Key concepts about DNA replication, including the Meselson-Stahl experiment, DNA synthesis, and the roles of leading and lagging strands. Topics include Okazaki fragments and proofreading mechanisms.