bio275 test 2

4. How does the total number of replication origins in bacterial cells compare with the number of origins in human cells?

1 vs 10,000

The following segment of DNA is from a transcribed region of a chromosome. You know that RNA polymerase moves from left to right along this piece of DNA, that the promoter for this gene is to the left of the DNA shown, and that this entire region of DNA is made into RNA. 5′-GGCATGGCAATATTGTAGTA-3′ 3′-CCGTACCGTTATAACATCAT-5′ Given this information, a student claims that the RNA produced from this DNA is: 3′-GGCATGGCAATATTGTAGTA-5′ Give two reasons why this answer is incorrect.

1) The RNA molecule should have uracil instead of thymine bases. 2) the polarity of the molecule is incorrectly labeled. The correct RNA molecule produced, using the bottom strand of the DNA duplex as a template, would be: 5'-GGCAUGGCAAUAUUGUAGUA-3'

16. Even though DNA polymerase has a proofreading function, it still introduces errors in the newly synthesized strand at a rate of 1 per 107 nucleotides. To what degree does the mismatch repair system decrease the error rate arising from DNA replication?

100-fold

5. The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster in prokaryotes. How much faster is it?

10X

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

2

You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′ 3′-TATCCGTAAGCTAGGCCTATCGTA-5′ Which of the following RNA molecules could be transcribed from this piece of DNA?

5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′

Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site?

5′-CCA-3′

B. What proportion of its progeny would you expect to contain the mutation after three more rounds of DNA replication and cell division?

A quarter or 25%. At the next round of DNA replication and cell division, the bacterium carrying the mismatched C-T will produce and pass on one normal DNA molecule from the undamaged strand containing the T and one mutant DNA molecule with a fully mutant C-G base pair. So at this stage, one out of the four progeny of the original bacterium is mutant. Subsequent cell divisions of these mutant bacteria will give rise only to mutant bacteria, while the other bacteria will give rise to normal bacteria. The proportion of progeny containing the mutation will, therefore, remain at 25%.

1. Give a reason why DNA makes a better material than RNA for the storage of genetic information, and explain your answer.

DNA is double stranded and therefore the complementary strand provides a template from which damage can be repaired accurately.

Is this statement true or false? Explain your answer. "Since introns do not contain protein-coding information, they do not have to be removed precisely (meaning, a nucleotide here and there should not matter) from the primary transcript during RNA splicing."

False. Although it is true that the sequences within the introns are mostly dispensable, the introns must still be removed precisely because an error of one or two nucleotides would shift the reading frame of the resulting mRNA molecule and change the protein it encodes.

Which of the following statements about RNA splicing is false?

For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene.

During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized DNA strand. Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and reproduce. A. After this original bacterium has divided once, what proportion of its progeny would you expect to contain the mutation?

Half or 50%. DNA replication in the original bacterium will create two new DNA molecules, one of which will now carry a mismatched C-T base pair. So one daughter cell of that cell division will carry a completely normal DNA molecule; the other cell will have the molecule with the mutation mispaired to a correct nucleotide.

Which of the following statements about DNA methylation in eukaryotes is false?

Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.

18. A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are deformed, but when they are interbred with each other, all their offspring are normal. Which two of the following statements could explain these results?

In the deformed mice, somatic cells but not germ cells were mutated. The toxic chemical affects development but is not mutagenic.

12. You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′-to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have?

It will fall off the template more frequently than the normal Exo+ polymerase.

Which of the following methods is not used by cells to regulate the amount of a protein in the cell?

Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

In a diploid organism, the DNA encoding one of the tRNAs for the amino acid tyrosine is mutated such that the sequence of the anticodon is now 5′-CTA-3′ instead of 5′-GTA-3′. What kind of aberration in protein synthesis will this tRNA cause? Explain your answer. (Hint: Think about the direction of the anti-codon)

Protein synthesis will stop prematurely.

Which of the following molecules is thought to have arisen first during evolution?

RNA

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon?

The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

Why is the old dogma "one gene—one protein" not always true for eukaryotic genes?

The transcripts from some genes can be spliced in more than one way to give mRNAs containing different sequences, thus encoding different proteins. A single eucaryotic gene, therefore, may encode more than one protein.

Which of the following statements is not an accurate statement about thymine dimers?

Thymine dimers are covalent links between thymidines on opposite DNA strands.

Which of the following statements about transcriptional regulators is false?

Transcriptional regulators usually interact with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix.

14. Because all DNA polymerases synthesize DNA in the 5′-to-3′ direction, and the parental strands are antiparallel, DNA replication is accomplished with the use of two mechanisms: continuous and discontinuous replication. Indicate whether the following items relate to (1) continuous replication, (2) discontinuous replication, or (3) both modes of replication.

__3___ primase ___2___ single-strand binding protein ___3___ sliding clamp ___3___ RNA primers ___1___ leading strand ___2___ lagging strand ___2___ Okazaki fragments ___3___ DNA helicase ___2___ DNA ligase

17. Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired?

a nick in the new strand

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?

by looping out the intervening DNA between their binding site and the promoter

6. DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction?

hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi

22. Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have _______________________.

inherited a mutation in a gene required for mismatch repair.

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking helicase were used to make the cell extracts?

initiation of DNA synthesis

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts?

initiation of DNA synthesis

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking single-strand binding protein were used to make the cell extracts?

initiation of DNA synthesis

13. A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate with the yeast DNA. Where do you think the block to replication arises? Choose the protein or protein complex below that is most probably responsible for the failure to replicate bacterial DNA. Give an explanation for your answer.

initiator proteins

8. What part of the DNA replication process would be most directly affected if a strain of bacteria lacking the exonuclease activity of DNA polymerase were used to make the cell extracts?

lagging-strand completion

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause?

substitution of lysine for isoleucine

A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals while a white blood cell defends the body against infection. This is because ______.

the neuron expresses some mRNAs that the white blood cell does not.

For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called _______. Various kinds of RNA are produced, each with different functions. ____ molecules code for proteins, __tRNA__ molecules act as adaptors for protein synthesis, ___ molecules are integral components of the ribosome, and ______ molecules are important in the splicing of RNA transcripts.

translation mRNA tRNA rRNA snRNA

19. Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication?

TTAT

Which of the following statements about the Lac operon is false?

The Lac repressor binds when lactose is present in the cell.

Investigators performed nuclear transplant experiments to determine whether DNA is altered irreversibly during development. Which of the following statements about these experiments is true?

The embryo that develops from the nuclear transplant experiment is genetically identical to the donor of the nucleus.

Which of the following statements about sequence proofreading during DNA replication is false?

The exonuclease activity cleaves DNA in the 5′-to-3′ direction.

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used to make the cell extracts?

leading-strand elongation

8 Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant?

mRNA

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?

methionine would be incorporated into proteins at some positions where leucine should be

Which of the following statements about miRNAs is false?

miRNAs are produced from rRNAs.

Explain 2 ways in which gene expression is halted at the mRNA level in eukaryotic cells. You cannot use siRNA/RNAi since it is in the next question.

miRNAs silence gene expression by repressing protein synthesis/promoting mRNA decay unsuccessful modifications capping, polyadenylation, splicing

According to current thinking, the minimum requirement for life to have originated on Earth was the formation of a _______________.

molecule that could catalyze its own replication.

When using a repeating trinucleotide sequence (such as 5′-AAC-3′) in a cell-free translation system, you will obtain:

peptides made up of three different amino acids in random order