BIO Ch.16

Which of the following are considered parts of the lac operon?

-Genes required for utilization of lactose -Regulatory regions of the operon (promoter and operator) -Repressor gene (lacI)

Which of the following statements about proteins in cells is true?

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

Where is the trp repressor gene located?

Outside the trp operon

Which of the following is a shared property of all DNA-binding motifs?

They can interact with the major groove of DNA.

The production of a functional miRNA begins in the nucleus and ends in the ______ of the cell.

cytoplasm

siRNAs are usually produced in the cell from long ________-stranded RNA molecules.

double

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

editing

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

The ______ motif is a nearly identical sequence of 60 amino acids found in many proteins that regulate development in eukaryotes.

homeodomain

The __________ motif is a nearly identical sequence of 60 amino acids found in many proteins that regulate development in eukaryotes.

homeodomain

Proteins that play a critical role in the development of many eukaryotic organisms usually have a highly conserved DNA-binding motif called the

homeodomain motif

Nonsense-mediated decay is a cellular response that recognizes and destroys

mRNAs with premature stop codons

In humans, DNMT1 acts as a _________ ________, an enzyme that can add methyl groups to bases in newly replicated DNA molecules.

maintenance methylase

In general, it has been found that histones in inactive regions of chromatin are

methylated

Which of the following are modifications that have been documented during RNA editing?

-Chemical modification of bases that change their base-pairing properties -Insertion of uracil residues

Which of the following are reasons why eukaryotes have a more complex gene regulation than prokaryotes?

-Eukaryotic DNA is organized into chromatin. -In eukaryotes, transcription occurs in the nucleus, while translation occurs in the cytoplasm.

Select the statements that are true about ubiquitin.

-It can be in the form of longer chains attached to other proteins. -It is made of 76 amino acids. -It can exist as an isolated molecule.

Which of the following describe the action of the enzyme ubiquitin ligase?

-It requires ATP which is hydrolyzed to ADP. -It adds a longer chain of ubiquitin to a protein in a stepwise fashion.

In the following list, choose all that are components of the eukaryotic transcription complex.

-Specific transcription factors -RNA polymerase II -Mediators and co-activators -General transcription factors

What are some lines of evidence that suggest that small RNAs may have initially evolved to protect the genome?

-They can be used by cells to degrade viral RNA. -In some animals they are involved in the silencing of transposons in the germline.

Select ways in which the initiation of translation can be regulated

-Translation factors can be modified. -Translation repressor proteins can block translation initiation.

Which of the following RNA molecules act in post-transcriptional gene regulation?

-siRNA -miRNA

What percentage of the total mRNA produced as primary transcript exits the nucleus?

5%

Based on our current knowledge, about what proportion of exons in primary transcripts leave the nucleus of a eukaryotic cell?

50%

What is an operon?

A cluster of genes controlled by a single promoter

One of the first miRNA that was discovered by scientists involves the lin-4 gene of C. elegans. The product of the lin-4 gene is which of the following?

A miRNA that inhibits the translation of the lin-14 gene because it is complementary to lin-14 mRNA

One class of chromatin-remodeling complexes function as molecular motors that modify DNA and histones. These complexes use energy released during the hydrolysis of

ATP

Which type of histone modification is usually correlated with active regions of chromatin?

Acetylation

The production of different mature mRNAs from the same primary transcript is called which of the following?

Alternative splicing

How can proteins interact with DNA and recognize DNA sequences without unwinding the DNA double helix?

By interacting with the major groove of the double helix

Specific transcription factors called activators have a domain organization: they contain a ________-binding domain and a separate _______ domain which are essentially independent of each other.

DNA, activating

Which of the following statements about mRNAs in prokaryotes and eukaryotes is true?

Eukaryotic mRNAs are typically much more stable than prokaryotic mRNAs.

In eukaryotes, gene regulation is geared toward maintaining which of the following?

Homeostasis

In the absence of tryptophan, which of the following describes the trp repressor?

It cannot bind the operator.

Match the structural gene in the lac operon with the enzyme it produces.

LacZ-B galactosidase LacY-permease LacA-transacetylase

Which of the following statements most accurately describes the function of the proteasome?

Proteins marked with ubiquitin enter one end of the proteasome and exit the other end as amino acids or peptide fragments.

Which statement accurately describes the production and degradation of proteins in a cell?

The production and degradation of each protein in a healthy is carefully regulated to ensure the proper functioning of the cell.

What would be the effect of swapping the DNA-binding domain of a eukaryotic activator with a different DNA-binding domain?

The specificity of the activator will change without affecting its ability to activate transcription.

In addition to a DNA-binding motif, regulatory proteins have a domain that allows interaction with which of the following?

The transcription apparatus

What is the function of a promoter in eukaryotic cells?

They are binding sites for general transcription factors which recruit RNA polymerase in order to initiate transcription.

Which of the following describes miRNAs and siRNAs?

They are small RNA molecules that are involved in posttranscriptional gene expression control.

How do bacterial regulatory proteins mediate negative control of transcription?

They decrease the frequency of transcription initiation by RNA polymerase

How do mediators and co-activators act?

They first bind a transcription factor and then bind another part of the transcription apparatus.

Recent studies suggest that small RNAs may have evolved for which of the following functions?

To protect the genome

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

Transcription initiation

miRNAs were discovered during studies of the lin-4 gene in C. elegans; this gene encodes for which of the following?

Two small RNAs (22 and 61 nucleotides, respectively)

Which of the following statements accurately describes glucose repression in bacteria.

When both glucose and lactose are present, the lac operon is not induced and bacteria will only use the glucose.

When a DNA molecule is replicated, it is hemimethylated. Soon after, the newly made DNA strand is methylated by

a maintenance methylase

A cluster of genes that are part of a single transcription unit under the control of a single promoter

a operon

A typical zinc finger motif is made of

an α-helical segment linked to a β-sheet segment by a zinc atom

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

chromatin

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

environmental

Changes in gene expression in prokaryotes are tightly linked to changes in the environment. For that reason almost all of the changes are

fully reversible, depending on environmental conditions

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 fission yeast, plants, and Drosophila, small RNAs and the RNA silencing pathways have been implicated in the formation of

heterochromatin

Some coactivators can affect the structure of chromatin by acting as

histone acetylases

Some corepressors that alter chromatin structure have been shown to act as

histone deacetylases

Proteins can recognize specific base pair sequences in DNA without unwinding the double helix by interacting with the ________ _______of the helix.

major groove

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

mediators

Cells have a response to shortened proteins called _________-_________ decay that recognizes and destroys mRNAs with premature stop codons.

nonsense mediated

The RNA interference pathway in which type of organism is much more complex than that of animals and can be involved in heterochromatin formation?

plants

When a regulatory protein's activity results in an increase in the frequency of transcription initiation, the protein is exerting

positive control

The first step in the biogenesis of miRNAs is the production of the

pri-miRNA

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

Large complexes of proteins that include enzymes that can modify histones, DNA and chromatin structure itself are known as chromatin-________ complexes.

remodeling

In general, mRNAs targeted by siRNAs are cleaved by RISC because

siRNAs have a near-perfect complementarity with their target

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

splicing

RNA polymerase II, together with all of the general and specific transcription factors and associated mediators and co-activators, form the eukaryotic

transcription

In both prokaryotes and eukaryotes, gene regulation most commonly occurs at the level of

transcription initiation

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

With its α-helix segment, a ________ finger motif can recognize the ________ groove of DNA.

zinc, major