bio ch 16

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

5%

Which organism has the simplest transcription regulation?

A bacterium, such as E. coli

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

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?

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

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

Translation

Select ways in which the initiation of translation can be regulated.

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

True or false: All mRNAs in a eukaryotic cell have a similar half-life of about 10 hours.

false

What is an operon?

A cluster of genes controlled by a single promoter

Which of the following describes a DNA-binding motif?

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

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

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

Alternative splicing

Which of the following are forms of post-transcriptional regulation in eukaryotes?

Alternative splicing RNA editing RNA interference mRNA degradation rate

The miRNA in the nucleus is cleaved by a nuclease called _____ that trims the miRNA to just a stem-and-loop structure which is now called _____.

Drosha; pre-miRNA

Almost 2000 miRNAs have been identified in various organisms including humans and _____ (give genus), the fruit fly. Listen to the complete question

Drosophila

Which of the following describes the control of the initiation of transcription?

Either positive or negative

Coactivators can affect the structure of chromatin by acting as which of the following?

HIstone acetylases

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

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 II to a promoter are called which of the following?

General transcription factors

Which of the following statements about the different kinds of mRNAs in eukaryotic cells is true?

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

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

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

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

It cannot bind its operator.

The RNA interference pathway in this type of organism is much more complex than that of animals.

Plants

An operon is derepressed when which of the following occurs?

The repressor alone cannot bind to the operator

Small RNAs may have evolved for which of the following functions?

To protect the genome

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.

What is the order of the lac genes following the operator?

Z, Y, A

The lac repressor binds to the lac operon when lactose is (present/absent) and the trp repressor binds to the trp operon when tryptophan is (present/absent).

absent; present

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 effector 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 inosine) are examples of RNA

editing

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

environmental

miRNAs were first discovered in a group of organisms called

nematodes

True or false: Even though we have little evidence, it is believed that the transport of mRNAs out of the nucleus is a potential site of gene regulation.

true

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

true

Which type of eukaryotic transcription factors can increase the level of transcription in certain cells in response to signals?

Specific transcription factors

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

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

Which of the following is a mechanism by which glucose represses the expression of the lac operon?

Glucose inhibits the production of cAMP, thereby preventing the activation of the lac operon.

Some corepressors that alter chromatin structure have been shown to act as which of the following?

Histone deacetylases

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

Homeostasis

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 are the requirements for gene transcription to be initiated in prokaryotic and eukaryotic cells?

RNA polymerase is key to transcription, and it must have access to the DNA helix and must be capable of binding to the gene's promoter for transcription to begin.

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

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

A class of chromatin-remodeling complexes that function as molecular motors that modify DNA and histones are dependent on what molecule?

atp

How do mediators and co-activators act?

by binding to the transcription factor and then binding to another part of the transcription apparatus.

Addition of ubiquitin marks proteins for which of the following?

degradation

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

Chromatin undergoes an _____ alteration when the alteration persists in the absence of a stimulus and is passed to daughter cells during cell division.

epigenetic

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

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

High levels of DNA methylation correlate with which of the following?

inactive genes, and the allele-specific gene expression seen in genomic imprinting

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

Which part of the eukaryotic cell contain digestive enzymes?

lysosomes

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

tryptophan

When protease is not actively breaking down proteins where is it stored in the eukaryotic cell?

Lysosome

Transcription regulation in eukaryotes is how complex as compared to transcriptional regulation in prokaryotes?

Much more

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.

Repressors are which type of molecules?

Proteins

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

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

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

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

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

siRNA miRNA

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

splicing

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

transcription

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

transcription

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

What is the function of the genes that are expressed in the lac operon of E. coli?

The utilization of lactose

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

These DNA-binding motifs share the property of interacting with specific sequences of bases, usually through the major groove of the DNA helix.

DNA _____ was the first modification of chromosome structure shown to act epigenetically.

methylation

The repressor of the lac operon binds to the region called the

operator

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.

operons

Where is the trp repressor gene located?

outside the trp operon

Proteins that have a ubiquitin chain attached to them are called _____ proteins.

polyubiquitinated

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

The short half-life of mRNAs for regulatory proteins is crucial for which reason?

It enables the cell to change the levels of those proteins very rapidly.

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

When the lac repressor is bound to the operator region of DNA which of the following enzymes is prevented from binding to the promoter region?

RNA polymerase

Which of the following describes the regulation of the lac and trp operons in bacteria?

The lac and trp operons are negatively controlled by a repressor protein.

Choose all ways in which glucose represses the utilization of lactose in glucose repression.

The presence of glucose leads to low level of cAMP. The presence of glucose inhibits the transport of lactose in the cell (inducer exclusion).

The binding of the corepressor to the trp repressor results in what?

The repressor binds to the operator and prevents transcription.

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

The transcription apparatus

Which of the following describes miRNAs and siRNAs?

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

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

major groove

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

major groove

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

proteasome

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

remodeling

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 of the following is a 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.

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 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

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)