Chap. 16 and 17 Study Set: Gene Expression and Biotech.

How many times does a restriction enzyme cut a double stranded piece of DNA at a given restriction site?

2

Select the true statements about the control of the trp operon 1. When tryptophan levels are low, the corepressor (tryptophan) binds to the repressor and transcription of the trp operon is blocked 2. When tryptophan levels are high, the corepressor (tryptophan) binds to the repressor and transcription of the trp operon is blocked 3. When tryptophan levels are high, the repressor is inactive and the trp operon is transcribed 4. When tryptophan levels are low, the repressor is inactive and the trp operon is transcribed

2 and 4

High levels of DNA methylation correlate with which of the following? 1. Areas of significant mutations 2. Allele-specific gene expression seen in genomic imprinting 3. Active genes 4. Inactive genes

2 and 4 2. Allele-specific gene expression seen in genomic imprinting 4. Inactive genes

The lac operon is controlled by two main proteins. These proteins___?

Act in the opposite fashion, one negative and one positive

The lac repressor, the trp repressor, and CAP are all___?

Allosteric proteins that bind to DNA and an effector

Repression in the trp operon and induction in the lac operon are both mechanisms that___?

Allow the cell to control the level of enzymes to fit environmental conditions

Eukaryotic mRNAs differ from prokaryotic mRNAs in that they___?

Are not co-linear with the genes that encode them

In eukaryotes, the regulation of gene expression occurs___?

At the level of transcription initiation, or posttranscriptionally

Which of the following statements is accurate for DNA replication in your cells, but not PCR? A. DNA primers are required B. DNA polymerase is stable at high temperatures C. Ligase is essential D. dNTPs are necessary

C. Ligase is essential

Specific transcription factors in eukaryotes interact with enhancers, which may be a long distance from the promoter. These transcription factors then___?

Can interact with the transcription apparatus via DNA looping

You study a gene known to be important in the early stages of heart development. Loss of the gene is also suspected to play a role in triggering lung cancer. What kind of transgenic mouse would you use to study your gene in vivo?

Conditional knockout

In the cell cycle, cyclin proteins are produced in concert with the cycle. This likely involves___?

Control of initiation of transcription of cyclin genes, and ubiquitination of cyclin proteins

In terms of studying gene function, what is the main benefit that genome editing has over RNAi?

Genome editing can eliminate gene function, RNAi simply reduces the levels of gene products

The difference between regulatory proteins with leucine zipper and helix-turn-helix DNA binding motifs?

Proteins with leucine zippers have two different recognition helices, while proteins with helix-turn-helix motifs are made of two identical units.

FISH analysis of a breast tumor biopsy for HER2 gene reveals two spots of fluorescence in cells. What conclusion do these data support about the tumor?

The HER2 gene is not amplified, and so particular treatments targeting the HER2 protein may not be suitable

MicroRNAs and short-interfering RNAs regulate gene expression at what level?

Translation

True or False: Small RNAs likely evolved to protect the genome.

True

Co-activators and ____ act by binding transcription factors and then binding another part of the transcription apparatus.

mediators

In some cases, the initiation of translation is regulated when ____ _____ proteins bind to the beginning of an mRNA so that the mRNA cannot attach to the ribosome.

translation repressor

The trp operon in E. coli contains information for the making of proteins responsible for the synthesis of _____.

tryptophan

Chromatin can be altered in a number of ways, such as histone modification and DNA methylation. When are such alterations considered to be epigenetic?

when they are inherited through cell division and when they persist in the absence of the initiation stimulus

Where does a cell get the double-stranded RNA needed to produce siRNAs 1. Viral infection 2. from the cell itself 3. bacterial infection

1 and 2 1. Viral infection 2. From the cell itself

Select ways in which the initiation of translation can be regulated. 1. Translation factors can be modified 2. Translation repressor proteins can block translation initiation 3. tRNAs can be targeted for degradation 4. Ribosome degrading proteins can prevent ribosomes from assembling

1 and 2 1. translation factors can be modified 2. translation repressor proteins can block translation initiation

Choose the different types of sequences that are typically spotted on a gene chip: 1. Short DNA probes 2. Short DNA sequences produced by PCR or RT-PCR 3. Short chemically synthesized RNA probes 4. Whole chromosomes

1 and 2 Short DNA probes Short DNA sequences produced by PCR or RT-PCR

Which of the following RNA molecules act in post-transcriptional gene regulation? 1. miRNA 2. siRNA 3. rRNA 4. RISC 5. tRNA

1 and 2 miRNA, siRNA

Which of the following describe the action of the enzyme ubiquitin ligase? 1.it adds a longer chain of ubiquitin to a protein in a stepwise fashion 2. it removes ubiquitin molecules from proteins which have been marked for degradation by mistake 3. it requires ATP which is hydrolyzed to ADP 4. it is found in the protease where it is responsible for the recycling of ubiquitin

1 and 3

Select the activities of ATP-dependent chromatin remodeling factors. 1. Histone replacement 2. Nucleosome phosphorylation 3. Nucleosome displacement 4. Nucleosome sliding 5. Nucelosome remodeling 6. Nucleosome adenylation

1, 3, 4, 5

Which of the following are forms of post-transcriptional regulation in eukaryotes? 1. Alternative splicing 2. DNA methylation 3. RNA interference 4. mRNA degredation rate 5. RNA editing 6. Histone acetylation

1, 3, 4, 5 Alternative splicing, RNA interference, mRNA degradation rate, and RNA editing

In the following list, choose all that are components of the eukaryotic transcription complex 1. General transcription factors 2. Histones 3. mRNA transcript 4. Specific transcription factors 5. RNA polyermase 2 6. Mediators and co-activators

1, 4, 5, 6

What is true about ubiquitin?

1,2,3 1. it can exist as an isolated molecule 2. it is made of 76 amino acids 3. it can be in the form of longer chains attached to other proteins

Place the following elements in the lac operon as they are organized on the chromosome. Start at the top with the gene/site that follows the gene for the repressor protein (lacl).

1. CAP site 2. Plac (promoter) 3. O (operator) 4. lacZ 5. lacY 6. lacA

Regulatory proteins that bind DNA typically recognize a specific DNA sequence about how many nucleotides in length?

10-15

Which of the following are the two basic categories of proteins that become ubiquitinated in the cell? 1. proteins that are produced by accident 2. proteins that are improperly folded or nonfunctional 3. proteins that are produced and degraded in a controlled fashion 4. exogenous proteins that are toxic to the cell

2 and 3

Select mechanisms that regulate the rate of degradation of mRNAs in the eukaryotic cell. 1. Translation repressors such as aconitase 2. Sequences near the 3' tail that make them targets for RNA-degrading enzymes 3. Sequences near the 3' end of mRNA that promote tail removal 4. RNA editing that leads to the appearance of a new stop codon

2 and 3 2. Sequences near the 3' tail that make them targets for RNA-degrading enzymes 3. Sequences near the 3' end of mRNA that promote tail removal

Select ways in which the loss of the poly-A tail of an mRNA promotes its quick degradation. 1. Loss of the tail leads to degradation by RNA endonucleases 2. Loss of the tail leads to degradation by 3' to 5' RNA exonucleases 3. Loss of the tail stimulates ubiquitination of the mRNA which tags it for degradation 4. Loss of the tail stimulates cap removal, which leads to degradation by 5' to 3' RNA exonucleases

2 and 4 2. Loss of the tail leads to degradation by 3' to 5' RNA exonucleases 4. Loss of the tail stimulates cap removal, which leads to degradation by 5' to 3' RNA exonucleases

Some corepressors that alter chromatin structure have been shown to act as which of the following? 1. Histone demethylases 2. Histone deacetylases 3. Histone methylases 4. Histone acetylases

2. Histone deacetylases

Which of the following statements about the different kinds of mRNAs in eukaryotic cells is true? 1. In general, mRNAs for regulatory proteins have much longer half-lives. 2. In general, mRNAs for regulatory proteins have much shorter half-lives. 3. Virtually all mRNAs in a eukaryotic cells have a similar half-life and are very stable.

2. In general, mRNAs for regulatory proteins have much shorter half-lives.

In addition to a DNA-binding motif, regulatory proteins have a domain that allows interaction with which of the following? 1. The replication apparatus 2. The transcription apparatus 3. The translation apparatus 4. The cytoskeleton

2. The transcription apparatus

Which of the following describes a DNA-binding motif? 1. A protein the recognizes a specific motif in the sequence of a DNA double helix 2. A specific sequence within the DNA where proteins can bind 3. A common three-dimensional structure which can interact with DNA and is found in many proteins

3. A common 3-dimensional structure which can interact with DNA and is found in many proteins

Many regulatory proteins have been described in both prokaryotes and eukaryotes. Which of the following statements about the DNA-binding motifs of those proteins is true? 1. There are probably as many different DNA-binding motifs as there are regulatory proteins. 2. There are even more DNA-binding motifs than there are regulatory proteins. 3. Despite their large diversity, regulatory proteins employ one of a small set of DNA-binding motifs.

3. Despite their large diversity, regulatory proteins employ one of a small set of DNA-binding motifs.

Which of the following statements about mRNAs in prokaryotes and eukaryotes is true? 1. Prokaryotic mRNAs are typically much more stable than eukaryotic mRNAs 2. Most eukaryotic and prokaryotic mRNAs have similar half-lives. 3. Eukaryotic mRNAs are typically much more stable than prokaryotic mRNAs.

3. Eukaryotic mRNAs are typically much more stable than prokaryotic mRNAs.

Transcription factors that are necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase 2 to a promoter are called which of the following? 1. Specific transcription factors 2. Nonspecific transcription factors 3. General transcription factors

3. General transcription factors

Which part of the eukaryotic cell contain digestive enzymes? 1. Golgi apparatus 2. Smooth endoplasmic reticulum 3. Lysosome 4. Mitochondria

3. Lysosome

Which of the following statements about proteins in cells is true? 1. Cells contain many free proteases which are constantly, but slowly, degrading proteins, overall, that leads to controlled protein turnover 2. Old, unused proteins in the cell are usually excreted outside the cell, where they are degraded by extracellular proteases 3. Old unused proteins in the cell are removed by specialized structures in a controlled way

3. Old unused proteins in the cell are removed by specialized structures in a controlled way

Where is the trp repressor gene located? 1. Immediately following the genes for tryptophan synthesis. 2. Immediately before the genes for tryptophan synthesis. 3. Outside the trp operon 4. Between the promoter and the operator

3. Outside the trp operon

Which of the following is true about the DNA-binding motifs of different regulatory proteins? 1. Two proteins that have the same type of DNA-binding motif bind very similar DNA sequences. 2. Two proteins that have the same type of DNA-binding motif usually bind the same DNA sequence. 3. Two proteins that have the same kind of DNA-binding motif do not necessarily bind the same DNA sequence.

3. Two proteins that have the same kind of DNA-binding motif do not necessarily bind the same DNA sequence.

When is the trp operon derepressed? 1. When the expression of the trpl gene is inhibited. 2. When tryptophan levels are high and the repressor is inactivated. 3. When tryptophan levels fall and the repressor can no longer bind the operator. 4. When tryptophan levels are high and the repressor is activated by it's co-repressor.

3. When tryptophan levels fall and the repressor can no longer bind the operator.

Two different regulatory proteins that have that have the same type of DNA-binding motif are similar in which of the following? 1. The specific contacts they make with DNA 2. The specific amino acids of their DNA-binding motifs 3. The primary structure of their DNA-binding motifs 4. The three dimensional structure of their DNA-binding motifs

4. The three-dimensional structure of their DNA-binding motifs

If a PCR is started using 10 pieces of template DNA, how many pieces of DNA would there be after 10 cycles?

About 10,000

Regulation by small RNAs and alternative splicing are similar in that both___?

Act after transcription and act via RNA/protein complexes

What potential problems must be considered in creating a transgenic bacterium with the human insulin gene isolated from genomic DNA to produce insulin? A. The genetic code of bacteria is significantly different from the genetic code of humans B. The bacterial cell will be unable to posttranslationally process the insulin peptide sequence C. There is no way to get the bacterium to transcribe high levels of a human gene D. Both A and B present problems

B. The bacterial cell will be unable to posttranslationally process the insulin peptide insulin

Regulatory proteins interact with DNA by____?

Binding to the major groove of the double helix and interacting with base-pairs

How can enhancers stimulate transcription despite being located far away from the genes they regulate?

DNA can bend and form a loop bringing the enhancer close to the promoter

Prokaryotic gene regulation is geared toward responding to changes in the ____; in multicellular eukaryotes, gene regulation is critical for directing _____ and maintaining_____?

Environment, development, homeostasis

Regulatory proteins stimulate transcription by which of the following methods?

Facilitating the binding of RNA polymerase to the promoter

True or False: Typically, once a protein is synthesized in a healthy cell, it will perform its function indefinitely because the cell environment is highly controlled.

False

DNA molecules can be separated based on their size using ___ ____.

Gel electrophoresis

In eukaryotes, binding of RNA polymerase to a promoters requires the action of____?

General transcription factors

In the trp operon, the repressor binds to DNA___?

In the presence of trp

In prokaryotes, control of gene expression usually occurs at the____?

Initiation of transcription

Regulatory proteins are proteins that do which of the following?

Modulate the ability of RNA polymerase to bind to the promoter.

In E. coli, induction in the lac operon and repression in the trp operon are both examples of____?

Negative control by a repressor

A mechanism of control in E. coli not discussed in this chapter involves pausing of ribosomes, allowing a transcription terminator to form in the mRNA. In eukaryotic fission yeast, this mechanism should___?

Not occur as transcription occurs in the nucleus and translation in the cytoplasm

In order for a gene to be transcribed, ____ polymerase must have access to the DNA double helix and be able to bind the gene's ____?

RNA, promoter

The development of which technology led to the entire field of biotechnology?

Recombinant DNA

You set up four RT-qPCR reactions all containing the same amount of total RNA. When the reactions are complete, you see that you have 10,000 units of fluorescence after 20 cycles for sample A, after 25 cycles for sample B, after 18 cycles for sample C, and after 22 cycles for sample D. Which of the samples had the most copies of target mRNA at the start of the RT-qPCR?

Sample C

The Ti plasmid of Agrobacterium usually induces tumors called galls on infected plants. When Agrobacterium is used to make transgenic plants, why does no gall form?

The gall-inducing genes are removed and replaced with the transgene

What is the basis of separation of different DNA fragments by gel electrophoresis?

The size of DNA fragments

What is a major difference between different DNA-binding motifs?

They employ different mechanisms to position and stabilize a recognition alpha helix in the major groove of DNA

In all cells, gene regulation most commonly happens at which level?

Transcription initiation

Golden rice is genetically modified to produce B-carotene which alleviates which deficiency?

Vitamin A

_____ (use the acronym) is the gene that initiates the inactivation process of one X-chromosome in mammalian females.

Xist (X-inactivation-specific transcript)

The protruding amino acid tails of histones in the nucleosome can be modified by the addition of _____ groups.

acetyl

_____ is the inducer of the lac operon.

allolactose

Gene ____, also known as DNA ____ consist of a solid surface, which has been spotted with hundreds to thousands of different DNA sequences.

chips, microarrays

In eukaryotes, DNA is organized into ____, which considerably complicates DNA-protein interactions during gene regulation.

chromatin

The process of producing a recombinant DNA molecule is often called molecular ____.

cloning

The purpose of gene therapy

defective genes are restored or replaced

When an operon is expressed because the repressor protein alone can't bind to the operator, the operon is said to be ____. In contrast, an operon can be _____ when an affector molecule inactivates the repressor.

derepressed, induced

Chemical modification of bases in the RNA to change their base-pairing properties (deamination of cytosine to uracil and deamination of adenine to ionsine) are examples of RNA ____.

editing

The 5-HT serotonin receptor in humans can exist in 12 isoforms. These isoforms are produced through RNA _____.

editing

Gene regulation allows bacteria to survive in response to _____changes, such as the availability of specific nutrients.

environmental

Most multicellular organisms execute complex developmental programs that ensure the production of functioning organisms; these developmental programs are heavily dependent on coordinated changes in ____ _____.

gene expression

Eukaryotic promoters are binding sites for ____ transcription factors.

general

In E. coli the lac operon is (induced/repressed) in the presence of lactose, and the trp operon is (induced/repressed) in the presence of tryptophan.

induced, repressed

Match the structural gene in the lac operon with the enzyme it produces: lacZ, lacY, lacA permease, transacetylase, B-galactosidase

lacZ-->B-galactosidase lacY-->permease lacA-->transacetylase

The short half-life of _____ transcripts for regulatory proteins is crucial as it enables the cell to change the levels of those proteins very quickly.

mRNA

Proteins can recognize specific base-pair sequences in DNA without unwinding the double helix by interacting with the ___ _____ of the helix.

major groove

Repressors are proteins that bind to regulatory sites on DNA called ____. These prevent transcription.

operators

A(n) ____ is a cluster of genes that are part of a single transcription unit that is under the control of a single promoter.

operon

In ____, the typical half-life of an mRNA transcript is 3 minutes, in contrast, mRNAs in _____ are usually very stable.

prokaryotes; eukaryotes

In _____ cells regulation allows rapid response to changes in the environment; in _____ cells, gene regulation is critical for maintaining homeostasis.

prokaryotic, eukaryotic

Proteins marked with ubiquitin enter the ____ at one end and exit the other side as amino acids or polypeptide fragments.

proteasome

The cell pathway during which ubiquitinated proteins are degraded and the ubiquitin itself is cleaved into units to be resused is called the ubiquitin- _____ pathway.

proteasome

A single DNA molecule made from two different sources is called ___DNA

recombinant

Glucose _____ occurs when bacterial cells are grown in the presence of glucose and lactose. In the presence of both sugars, bacteria will preferentially use the glucose before using the lactose.

repression

In bacteria ____ occurs when organisms capable of making biosynthetic enzymes do not produce them.

repression

In Drosophila, sex determination involves a series of alternative ____ events, which differ in males and females.

splicing

The process whereby different transcripts are made from a single gene is called alternative ____.

splicing

Which is the purpose of transformation?

to introduce new DNA into a cell