Cell and Molecular Bio Chapter 6 Practice Problems

What would happen during DNA replication if DNA ligase was missing?

DNA ligase links the DNA fragments that are produces on the lagging strand. in the absence of ligase, the newly replicated DNA strands will remain as fragments but no nucleotides will be missing.

What would happen during DNA replication if sliding clamps for DNA polymerase were missing?

DNA polymerase will fall off the template. technically it could just rebind and continue but it would slow down the process as it will just keep falling off and keep needing to rebind itself.

What would happen during DNA replication if DNA helicase was missing?

DNA polymerase will stop because it cannon separate strands of the template DNA ahead of time so little or no DNA will be synthesized.

What effects would you expect of ddCMP were added under the same conditions?

Dideoxycytosine monophosphate (ddCMP) lacks the 5' triphosphate group as well as the 3' hydroxyl group of the sugar ring. It therefore cannot provide the energy that drives the polymerization reaction of nucleotides into DNA and therefore will not be incorporated into the replicating DNA. Addition of this compound should not affect DNA replication.

Okazaki fragments are removed by a nuclease that degrades RNA...TRUE or FALSE?

False, only the RNA primers are removed by an RNA nuclease. Okazaki fragments are pieces of newly synthesized DNA on the lagging strand that are eventually joined together by DNA ligase.

A bacterial replication fork is asymmetrical because it contains two DNA polymerase molecules that are structurally distinct...TRUE or FALSE?

False, the identical DNA polymerase molecules catalyze DNA synthesis on the leading and lagging strands of a bacterial replication fork. The replication fork is a symmetrical because the lagging strand is synthesized in pieces that are then stitched together.

DNA mismatch repair enzymes preferentially repair bases on the newly synthesized DNA strand, using the old DNA strand as a template. If the mismatches were simply repaired without regard for which strand served as template, would this reduce replication errors?

If the old strand were replaced using the new strand that contained the replication errors as a template, the error would become a permanent mutation in the genome. the old info would be erased. if a pair of enzymes did not distinguish between the 2 strands, there would be only a 50% chance that any given replication error would be corrected.

What would happen during DNA replication if nuclease that removes DNA primers was missing?

RNA fragments will remain attached to the newly replicated DNA fragments. ligase will not link DNA to RNA so ligation will not occur. The lagging strand will consist of fragments of both DNA and RNA.

What would happen during DNA replication if primase was missing?

RNA primers can't begin on either leading or lagging strand so DNA replication cannot begin.

In the absence of DNA repair, genes are unstable...TRUE or FALSE?

True, if a damaged nucleotide also occurred naturally in DNA, the repair enzyme would have no way of identifying the damage. It would only have a 50% chance of fixing the right strand.

Cancer can result from the accumulation of mutations in somatic cells... TRUE or FALSE?

True, usually multiple mutations of specific types need to accumulate in a somatic cell lineage to produce cancer. A mutation in a gene that codes for a DNA repair enzyme can make a cell more liable to accumulate further mutations thereby accelerating the onset of cancer.

The error rate of DNA replication id reduced both by proofreading by DNA polymerase and by DNA mismatch repair...TRUE or FALSE?

True, with proofreading DNA polymerase has an error rate of one mistake in 10^7 nucleotides polymerized. 99% of its errors are corrected by DNA mismatch repair enzymes...the final error rate is one mistake in every 10^9 nucleotides.

Explain why telomeres and telomerase are needed for replication of eukaryotic chromosomes but not for replication of circular bacterial chromosomes.

because DNA polymerase requires a 3' OH to synthesize DNA, without telomeres and telomerase the ends of linear chromosomes would shrink during each round of DNA replication. For bacterial chromosomes, which have no ends, the problem does not arise; there will always be a 3' OH group available to prime the DNA polymerase that replaces the RNA primer with DNA. Telomeres and telomerase prevent the shrinking of chromosomes because they extend the 3' end of DNA strand. This extension of the lagging strand template provides the 'space' to begin the final Okazaki fragments.

What would you expect of ddCTP were added to a DNA replication reaction in large excess over the concentration of the available deoxycytosine triphosphate (dCTP), the normal deoxycytosine triphosphate?

ddCTP is identical to dCTP except for it lacks the 3' hydroxyl group on the sugar ring. ddCTP is recognized by DNA polymerase as dCTP and becomes incorporated into DNA; because it lacks the 3' hydroxyl its addition to a growing DNA strand creates a dead end to which no further nucleotides can be added. so, if ddCTP is added in large excess, new DNA strands will be synthesized until the first G (complementary to C) is encountered on the template strand. ddCTP will then be incorporated instead of C and the extension of this strand will stop.

Describe the consequence that would arise if a eukaryotic chromosome lacked one or both telomeres?

it would lose nucleotides during each round of DNA replication and would gradually shrink. Eventually, essential genes would be lost and the chromosome's ends might be recognized by the DNA damage-response mechanisms, which would stop cell division or induce cell death.

Describe the consequence that would arise if a eukaryotic chromosome contained only one origin of replication at the exact center of the chromosome? at one end of the chromosome?

it would take more that 8 days to replicate the DNA. This rate would severely limit the rate of cell division. if the origin of replication were at one end the time required to replicate this chromosome would be about double.

What would happen during the DNA replication process if DNA polymerase was missing?

no replication can take place. RNA primers would be laid down at the origin of replication.

Would you still need telomeres and telomerase to complete eukaryotic chromosome replication if primase always laid down the RNA primer at the very 3' end of the template for the lagging strand?

telomeres and telomerase are still needed even if the lase fragment of the lagging strand were initiated by primase at the very 3' end of the chromosomal DNA, in as much as the RNA primer must be removed.

What would happen if ddCTP were added at 10% of the concentration of the available dCTP?

there would be a 1 in 10 chance of its being incorporated whenever a G is encountered on the template strand. Thus a population of DNA fragments will be synthesized and from their lengths one can deduce where the G residues are located on the template strand. This strategy forms the basis of methods used to determine the sequence of nucleotides in a stretch of DNA.

Describe the consequence that would arise if a eukaryotic chromosome had no centromere?

without centromeres, which attach mitotic chromosomes to the mitotic spindle, the two new chromosomes that result from chromosome duplication would not be partitioned accurately between the two daughter cells. Therefore, many daughter cells would die because they would not receive a full set of chromosomes.