exam 3 clickers and homeworks

Which steps occur during tRNA processing? 'CCA' sequence addition Base modification Poly-A tail addition Intron splicing 5' cap addition

'CCA' sequence addition Base modification Intron splicing

What are the steps of PCR testing?

1. The reaction mixture is heated to 94 °C. 2. The double-stranded DNA is denatured to form single-stranded DNA. 3. The temperature of the reaction mixture is lowered to allow the primers to anneal to the DNA template. 4. The reaction mixture is heated to 72°C. 5. Taq polymerase synthesizes new DNA.

If the top strand of this DNA is the template strand, which rNTP will be the last added to the RNA transcribed from this template? 5'-TAAACAATGGTCGACATTG-3' 3'-ATTTGTTACCAGCTGTAAC-5' A G C U

A

DNA polymerase I has 5'-3' polymerase activity, 5'-3' exonuclease activity, and 3'-5' exonuclease activity necessary for DNA replication. Mutations in the gene that encodes DNA polymerase I may cause the enzyme to lose these activities. A. Lost 5'-3' exonuclease activity ________ B. Lost 5'-3' polymerase activity _______ C. Lost 3'-5' exonuclease activity ______

A. RNA primer is not removed B. No DNA synthesis to fill gaps caused by RNA primer removal C. Loss of proofreading ability during DNA synthesis

What is the difference between alternative splicing and alternative tailing? Alternative splicing changes the sequence of nucleotides within an exon, while alternative tailing only shortens from the 3' end. Alternative splicing results in the production of miRNAs, alternative tailing does not. Alternative splicing can remove exons from the middle of a gene, alternative tailing can only remove exons from the end of a gene.

Alternative splicing can remove exons from the middle of a gene, alternative tailing can only remove exons from the end of a gene.

In the figure above (13.5 from your book), where is the promoter for Gene B? At location #1 At location #2

At location #2

Relaxes supercoiled DNA

DNA gyrase

Unwinds the two stands of template DNA

DNA helicase

Joins Okazaki fragments together by sealing gaps in the sugar-phosphate backbone

DNA ligase

Synthesizes new DNA

DNA polymerase III

If a mutation occurred in an enhancer sequence so that transcription factors no longer bound to it, which outcome would be most likely? Transcription would stop. No effect. Fewer transcripts would be made. More transcripts would be made.

Fewer transcripts would be made.

If the bottom strand is transcribed, what RNA molecule will result? Enter your answer from the 5' to the 3' direction. 5'- GCGTTATGCTAAG-3' 3'- CGCAATACGATTC-5'

GCGUUAUGCUAAG

After DNA replication in a human cell line (grown in vitro), each nucleus is enlarged, and the amount of DNA per cell greatly exceeds the expected amount of ~3.2 Gb. This is likely due to a defect in which protein or enzyme? Hint: Are humans prokaryotic or eukaryotic? DNA primase Helicase Geminin Telomerase

Geminin

Identify the statements that are true about prokaryotic and/or eukaryotic promotors. In eukaryotes, the promoter is recognized directly by RNA polymerase II. In both prokaryotes and eukaryotes, the promoter is located upstream from the transcription start site. In prokaryotes, the promoter contains consensus sequences at −35 and −10 upstream of the transcription start site. In both prokaryotes and eukaryotes, the rate of transcription can be increased through interactions with enhancer sequences. In eukaryotes, the promoter often contains a TATA box, which is where the TATA‑binding protein binds.

In eukaryotes, the promoter is recognized directly by RNA polymerase II. In both prokaryotes and eukaryotes, the promoter is located upstream from the transcription start site. In prokaryotes, the promoter contains consensus sequences at −35 and −10 upstream of the transcription start site. In eukaryotes, the promoter often contains a TATA box, which is where the TATA‑binding protein binds.

What functions does the 5' cap fulfill? Termination Increases the stability of the RNA molecule Ribosomal recognition Intron removal

Increases the stability of the RNA molecule Ribosomal recognition Intron removal

Interacts with the oriC sequence to unwind a short stretch of DNA

Initiator proteins

Which of the following are true about exons and introns? Introns are removed during mRNA processing. Every exon is translated into amino acids. Exons are present in mature mRNA. Introns are transcribed from DNA to RNA. The 5'-UTR and 3'-UTR are both introns.

Introns are removed during mRNA processing. Exons are present in mature mRNA. Introns are transcribed from DNA to RNA.

What role does the sigma factor play in prokaryotic transcription? It polymerizes RNA It recognizes the rut site It recognizes the promoter sequence It is a topoisomerase

It recognizes the promoter sequence

How are DNA fragments separated using gel electrophoresis? Larger DNA fragments move more slowly through the gel than smaller fragments. DNA fragments complementary to probes in the gel travel more slowly through the matrix. Negatively charged DNA fragments move through the gel more quickly. Smaller DNA fragments bind more strongly to the gel than do larger DNA fragments.

Larger DNA fragments move more slowly through the gel than smaller fragments.

A scientist attempts to amplify a short DNA fragment. She has template DNA and Taq polymerase. What else does she need? Helicase Primers dNTPs Ligase DNA polymerase I

Primers dNTPs

How does eukaryotic replication differ from prokaryotic replication? Telomerase is necessary to maintain telomere length in eukaryotes, but not prokaryotes. Theta replication is possible for circular prokaryotic chromosomes, but not for linear eukaryotic chromosomes. There are multiple replicons in eukaryotic replication, but only a single replicon in prokaryotic replication. Eukaryotic replication has Okazaki fragments, but prokaryotic does not.

Telomerase is necessary to maintain telomere length in eukaryotes, but not prokaryotes. Theta replication is possible for circular prokaryotic chromosomes, but not for linear eukaryotic chromosomes. There are multiple replicons in eukaryotic replication, but only a single replicon in prokaryotic replication.

What is the outcome of RNA editing? The mature mRNA can have a different sequence of nucleotides than the DNA from which it was transcribed. The mature mRNA can have poly-A tails of different length depending on the requirements for RNA stability. The mature mRNA can contain different exons, depending on which exons were removed during intron splicing. The mature mRNA can be different lengths, depending on the location of cleavage at the 3' end.

The mature mRNA can have a different sequence of nucleotides than the DNA from which it was transcribed.

Why do linear, eukaryotic chromosomes shorten with each round of replication? There is no existing 3' OH from which to initiate DNA synthesis after the RNA primer is removed. Single-stranded binding proteins cannot adhere to telomeric sequences. Linear chromosomes are replicated starting at one end, and replication often stalls before reaching the other end. The ribose sugars in the RNA primers are inherently unstable.

There is no existing 3' OH from which to initiate DNA synthesis after the RNA primer is removed.

What do siRNA and crRNA have in common? They are both produced by the Dicer protein. They complex with proteins to form RISC. They are integrated into the Cas protein. They can both destroy invading viral genomes.

They can both destroy invading viral genomes.

What role do primers play in a polymerase chain reaction? They terminate the reaction. They separate the strands of DNA. They provide a free 3'-OH from which to initiate DNA synthesis. They target or bracket the region of interest in the DNA.

They provide a free 3'-OH from which to initiate DNA synthesis. They target or bracket the region of interest in the DNA.

dNTPs are utilized during DNA synthesis, and the energy resulting form the cleavage of two of the three phosphate allows the formation of: a hydrogen bond between two nitrogenous bases. a reactive 2' OH group. a phosphodiester bond between two nucleotides.

a phosphodiester bond between two nucleotides.

The TATA box is part of the/a . . . regulatory promoter core promoter mediator transcription factor II D basal transcription apparatus

core promoter

an enhancer region is deleted

decreased transcription

the regulatory promotor is deleted

decreased transcription

Which of the following is NOT part of the basal transcription apparatus in eukaryotes? mediator protein transcription factors enhancer sequences RNA polymerase II

enhancer sequences

The Rat1 protein involved in transcription termination in eukaryotes has what enzymatic activity? ligase exonuclease proteinase polymerase helicase

exonuclease

In prokaryotes, transcription must be terminated before translation is initiated. True False

false, they can occur simultaneously

Which of the following is NOT a difference between replication and transcription? in transcription the 2' OH group of ribose is involved in the polymerization reaction to form a phosphodiester bond; in replication it's the 3' OH group of deoxyribose RNA polymerase does not require a primer to begin transcription, but DNA polymerase does require a primer to begin replication thymine is one of the four bases found in DNA; uracil replaces thymine in RNA in transcription only one strand of the double-stranded DNA molecule is used as template, while in replication both strands serve as templates

in transcription the 2' OH group of ribose is involved in the polymerization reaction to form a phosphodiester bond; in replication it's the 3' OH group of deoxyribose

Prevents single-stranded DNA from forming secondary structures

single-stranded binding proteins

Which of the following RNA types is found in both prokaryotes and eukaryotes? siRNA tRNA rRNA crRNA mRNA

tRNA, mRNA, rRNA

The sigma factor in prokaryotes is most similar to which of the following: The TATA box Enhancer sequences Transcriptional activator proteins Transcription factors

transcription factors

The TATA box is deleted.

very low or no transcription

the TATA-binding region is deleted

very low or no transcription