exam 2 bio

How many replication forks are formed when an origin of replication is opened?

2

Which of the following is a false statement regarding Polymerase Chain Reaction (PCR)?

A PCR reaction utilizes all of the enzymes that are used during cellular replication.

In assembling a nucleosome, normally the ... histone dimers first combine to form a tetramer, which then further combines with two ... histone dimers to form the octamer.

H3 and H4, H2A and H2B

What part of the DNA replication process would be most directly affected if your bacterial strain had a mutation in the gene for DnaA protein?

Initiation of DNA synthesis

What is the function of dideoxynucleotides in Sanger DNA sequencing?

They stop synthesis at a specific site, so the base at that site can be determined.

Nucleosomes are aided in their formation by the high proportion of

basic amino acids in histone proteins

You learn that a Mars lander has retrieved a bacterial sample from the polar ice caps. You obtain a sample of these bacteria and perform the same kind of experiment that Meselson and Stahl did to determine how the Mars bacteria replicate their DNA. Based on the following equilibrium density gradient centrifugation results, what type of replication would you propose for these new bacteria?

dispersive

nucleosomes are present in

eaukaryotic chromosomes

(blank) is less acetalated

heterochromatin

The genomes of many organisms have been sequenced. What benefits or uses could result from this information?

personalizing medicine based on individual genomic sequencetracing evolutionary history and relationships of organisms elucidating genetic patterns of medical interest dentifying genes of agricultural import

Which of the following enzymes or enzyme subunits does not rely on ATP hydrolysis for its correct function?

primase

When forensic scientists create a DNA profile they compare genetic markers from two or more DNA samples. What are they comparing?

subtle sequence variations in DNA between copies of homologous chromosomes.

Each replication fork requires both leading and lagging strand synthesis because

the DNA templates are antiparallel and yet the DNA polymerases only work in one direction.

On average, errors occur in DNA synthesis only once in every ten billion nucleotides incorporated. Which of the following contributes to this high fidelity of DNA synthesis?

A. Complementary base-pairing between the nucleotides. B. Exonucleolytic proofreading by the 3ʹ-to-5ʹ exonuclease activity of the enzyme to correct mispairing. C. A mismatch repair system

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They.....

A. can slide nucleosomes on DNA. B. have ATPase activity. C. can remove or exchange core histone subunits.

All of the following are true about histone chemical modification EXCEPT:

A. modifications almost always happen on the histone tails. B. modifications are irreversible. C. modifications can be re-established during replication. D. modifications are covalent. Answer: B

Bacterial and eukaryotic replication, have many similarities. Which of the following is not a true comparison?

Both have a primer made only of ribonucleotides, and then exhibit polymerase switching to the replicative polymerase. (Eukaryotes only)

DNA synthesis has taken place however multiple nicks in the lagging strand are observed. This bacterial strain has a mutation in the gene that encodes for the protein:

DNA ligase

Matthew Meselson and Frank Stahl determined that DNA replication is a semi-conservative process. Which of the following is an accurate description of daughter DNA duplexes after replication?

Each daughter DNA duplex consists of one parental strand and one newly synthesized strand.

Which of the following best describes mechanisms by which histones interact with DNA?

Interactions between histone core proteins and DNA occur through positive and negative charge interactions at the minor groove.

During which phase of the cell cycle would chromosomes be maximally condensed?

M phase mitosis

What is the "end replication problem" in eukaryotic linear chromosomes?

Once the last RNA primer on the lagging strand is removed DNA polymerase cannot fill in the gap.

What is the difference between orthologs and paralogs?

Orthologs are in different organisms; paralogs are in the same organism.

Suppose a chemist develops a new drug that neutralizes the positive charges on the tails of histone proteins. What would be the most likely effect of this new drug on chromatin structure if any?

Such a drug would be mimicking the effects of histone acetylation and loosen the chromatin structure.

What is responsible for the high processivity of the Pol III holoenzyme?

The β sliding clamp allows Pol III to stay associated with the DNA template as each nucleotide is added.

You set up a replication assay using bacterial cell extracts that contain all of the components that would be needed for replication. All of the components (initiator proteins DnaA, helicases, polymerases, primase etc are functioning properly). You use template DNA isolated from eukaryotic cells (devoid of nucleosomes) but fail to observe any replication. You realize why this won't work and fix the problem. Which one of these options below would be the solution that fixed why there was no replication?

You depleted the extracts of DnaA protein and replaced it with eukaryotic initiator proteins. [All other proteins have same functionality= however function of DnaA relies on recognixing DNA sequences or the origin which is different in bacteria and eukaryotes]

The first evidence for nucleosome formation came from limited digestion of chromosomal DNA with micrococcoal nuclease. Gel electrophoresis of the DNA after the reaction would have revealed:

a ladder of fragments about 200 bp apart.

To assay for replication (DNA synthesis) in a test tube you need to provide all four dNTPs with one of them labeled with radioactivity. You can then look for incorporation of the 'label/radioactivity' as a marker for synthesis. This is done by using a dNTP in which one of the 3 phosphates is the radioactive form- 32P. Which phosphate would you label for your assay to work?

alpha phosphate

While learning about histone modifications, you were introduced to the processes that can permit cells to have a "memory" of chromatin states during replication. Which of the following processes best describes a correct example of how this "memory" could be generated in the cell at the level of chromatin?

an old histone is modified with an acetyl group → a histone acetyl transferase proteins binds the old histone using its bromodomain → the adjacent new histone is acetylated restoring the chromatin state.

(blank) shows little to no gene expression

heterochromatin

H1 binding to DNA is different than that of the other four histones because H1 binds to:

one strand of the linker DNA as it comes off the nucleosome and binds a second site in the central region of the DNA supercoil.

During a sequencing reaction if the machine reads the newly synthesized strand as 5`-GATCATC-3` then which of the following represents the actual sequence of the template strand (in the 5` to 3` direction)?

C. 5` GATGATC 3`

Given this information, which of the following could describe the normal functioning of CBP?

CBP adds acetyl groups to the side chains of amino acids in histone tails, causing the chromatin to decondense and allowing access to previously hidden promoter regions.

Ciprofloxacin is an antibiotic used to treat multiple bacterial infections. Bacterial cells treated with Ciprofloxacin show increase in positive supercoiling of their chromosomal DNA. Given what you know about the role of different enzymes in prokaryotic DNA replication, which of the following enzymes is inhibited by Ciprofloxacin?

DNA gyrase

A nucleosome contains two molecules each of histones

H2A and H2B as well as H3 and H4

Which of the following statements about eukaryotic genomes is TRUE?

People differ, not only at millions of individual SNPs, but also in the number of copies of many larger segments of the genome

DNA synthesis has taken place, however there is presence of uracil in the DNA. This bacterial strain has a mutation in the gene that encodes for the protein:

RNAseH

One of the mutants is an "Exo- " mutant form of DNA polymerase in which the 3ʹ-to-5ʹ exonuclease function has been destroyed but the polymerizing activity is unchanged. Which of the following properties do you expect the mutant polymerase to have (when compared with normal)

Replicated DNA will hvae more DNA mismatched pairs

Observation of replication of circular bacteria DNA using autoradiography revealed which important general feature of DNA replication.

Replication initiates from a single origin, creating a single replication bubble in the plasmid

Pick the correct 2 statements from the options below

Telomeres are always heterochromatic Centromeres are never euchromatic

Which of the following describes the approximate chromosomal location of the termination of replication in bacteria?

Termination occurs at a location halfway around the chromosome.

Which of the following is true about the termination of replication in bacteria?

Termination occurs at sequences called Ter sites. B. Binding of Tus proteins to Ter sites blocks the advance of the replication fork. C. There are two clusters of Ter sites oriented in opposite directions. D. The association of Tus with Ter is polar; the replication forks can pass through the first set but are blocked by the second.

Which of the following best describes why Okazaki fragments are not observed in PCR?

The DNA template is completely denatured by near boiling temperatures and the oligonucleotide primers anneal to the ends of the fragment that is to be amplified thus allowing for DNA polymerase to synthesize the new strands in long continuous stretches.

Which of the following is TRUE regarding nucleosome formation during DNA replication?

The addition of some newly synthesized histones is a part of nucleosome assembly.

Suppose that an organism exhibits a mutation that results in continually active telomerase in the stomach tissue cells. Which of the following could be a result of this mutation?

The cells while have excessive growth, organism will be at risk for cancer

Which of the following definitions best describes the term 'chromatin'?

The complex of DNA and proteins that forms the eukaryotic chromosome

Which of the following statements correctly explains what it means for DNA replication to be bidirectional?

The replication forks formed at the origin move in opposite directions.

1.What would happen in one round of replication if the orientations of all the Ter sites in the chromosome were reversed.

The two replication forks would never meet, and part of the chromosome near the terminus would remain unreplicated.

If the amount of H1 increases in a region of chromatin, will gene expression (transcription of the gene) in that region increase or decrease? Why?

Transcription will decrease because an increase in H1 will lead to greater compaction of DNA.

In a typical sequencing reaction, the amount of ddNTP is much less than of the dNTPs. Predict the results if amount of ddNTP added to a reaction would be much greater than amount dNTPs. After gel electrophoresis and visualization you would see:

mostly short fragments would be present and only sequences very close to the primer could be read.