intro ch 19

What are the two structural domains that are found in all transcriptional activator proteins?

Activation domain DNA-binding domain

Eukaryotes have three RNA polymerases that are named RNA polymerase I, II, and III. Genes encoding proteins are transcribed by RNA polymerase ____ The major ribosomal RNAs are transcribed by RNA polymerase _____ while genes encoding the transfer RNAs (tRNAs) are transcribed by RNA polymerase

Blank 1: II or 2 Blank 2: I or 1 Blank 3: III or 3

The protein complex that serves as a bridge between RNA polymerase II bound at the promoter and activator or repressor proteins bound at an enhancer is called

Blank 1: Mediator, mediator, mediators, or mediater

Eukaryotic promoters often contain a conserved sequence of approximately seven nucleotides that is located just upstream of the transcription initiation site. This sequence is called a(n) _____ box.

Blank 1: TATA or initiation

Transcription factors that, when bound to an enhancer element, increase transcription of a gene above the basal level, are called transcriptional

Blank 1: activators

The term for the mechanism that enables two or more different polypeptide sequences to be produced from a single gene is

Blank 1: alternative, alternate, or alternative splicing Blank 2: splicing

In order to be recognized by the small ribosomal subunit, a eukaryotic mRNA is circularized through the interaction of the poly-A ____ _____ and eIF4G.

Blank 1: binding Blank 2: protein

The field of science that combines biology, computer science, and information technology into a single discipline is called

Blank 1: bioinformatics or bioinformatic

A protein that increases the rate of transcription by modifying chromatin structure but does not directly bind to the DNA itself is called a(n)

Blank 1: coactivator or coactivators

Histone acetyltransferases can act as transcription factor ____ because they can favor gene expression by acetylating certain lysine residues in histones.

Blank 1: coactivators

Many activators are composed of two protein subunits. To form a complete activator, each protein subunit must have a(n) _____ domain.

Blank 1: dimerization, dimer, dimerized, or dimeric

Activators and repressors are transcription factors that bind to DNA sequence elements called

Blank 1: enhancers or enhancer

The zinc finger motif is typically found in transcription factors in ____ cells, while the helix-turn-helix domain also occurs in transcription factors in ____ cells.

Blank 1: eukaryotic, eukaryote, or eukaryotes Blank 2: prokaryotic, prokaryote, or prokaryotes

When two different polypeptide subunits interact to form a transcription factor (such as, for example, Jun-Fos) the resulting transcription factors is a(n)

Blank 1: heterodimer or heterodimers

Some corepressors inhibit transcription by modifying amino acids in the tails of _____ proteins. Other corepressors interact directly with the RNA pol II basal complex and prevent it from binding to the ______

Blank 1: histone or histones Blank 2: promoter

The dimerization of two identical proteins results in a

Blank 1: homodimer or homodimers

Enhancer sequences can function at a distance from the promoter because the DNA between the enhancer and promoter will ____ to allow basal factors, Mediator, and activators to interact with one another.

Blank 1: loop, bend, or loops

Most proteins that bind to DNA fit within the ____ groove of the double helix.

Blank 1: major

Activators promote transcription by interacting with basal factors and RNA polymerase to recruit them to the _____ of a gene.

Blank 1: promoter or promoters

In multicellular eukaryotes, the differentiation of tissues and organs is controlled by gene ____

Blank 1: regulation, regulators, or regulator

In order for a corepressor protein to associate with an enhancer, a(n) ____ must be bound to the enhancer.

Blank 1: repressor

Transcription factors that bind to specific DNA sequences near genes and prevent transcription from occurring are called

Blank 1: repressors or repressor

Basal factors, activators, and repressors are collectively known as _____ factors

Blank 1: transcription or transcriptional

Two DNA-binding domains that are commonly found in transcription factors are the _____ finger and the _____-turn-____ domains.

Blank 1: zinc Blank 2: helix Blank 3: helix

Which domain of a transcription factor interacts with the basal complex or with coactivators?

Activation domain

What proteins bind to the promoter of a gene?

Basal transcription factors

What fields of study are included in bioinformatics?

Biology, computer science, and information technology

The two protein domains that are found in all activator proteins are the ____ -binding domain and the ____ domain.

Blank 1: DNA Blank 2: activation, activator, activating, or active

Eukaryotic repressors recruit _____ proteins to enhancers.

Blank 1: corepressor or corepressors

A regulatory protein that prevents transcription by interfering with the function of activators instead of by recruiting corepressors is called a(n) ______ repressor.

Blank 1: indirect

A DNA element that organizes chromatin so that enhancers have access only to particular promoters is called a(n)

Blank 1: insulator or insulators

Dimerization between two transcription factors can be mediated by a(n) ___ zipper.

Blank 1: leucine

Which of the following protein domains can be found in repressors?

Dimerization domain Repression domain DNA-binding domain

Which of the following statements best describes gene regulation in multicellular eukaryotes?

Each gene may contain several enhancer elements each with binding sites for several different transcription factors.

What is the source of the dsRNA that is processed to produce siRNA?

Either endogenous or exogenous RNA

In multicellular eukaryotes, what controls the elaboration of sex-related characteristics and behaviors?

Gene regulation

Which statement accurately describes the ability of histone modifying enzymes to bind specific DNA sequences?

Histone modifying enzymes cannot recognize and bind specific DNA sequences on their own.

Where is the TATA box of a eukaryotic gene located?

In the promoter

What is the function of a leucine zipper?

It allows proteins to dimerize with one another.

When a cell divides, most of the histone modifications are lost in the daughter cells. How can daughter cells reestablish their histone modifications?

Transcription factors bind to newly made DNA and recruit histone modifying enzymes.

What is the benefit of alternative splicing?

Two or more polypeptides can be derived from a single gene.

Which DNA-binding domain is most commonly found in eukaryotic proteins rather than in prokaryotic proteins?

Zinc finger

Corepressor proteins can bind to DNA only when ___

a repressor with which they can associate is already bound to DNA

The dimerization domain of an activator enables the activator to bind to _____.

another transcription factor subunit

The TATA box-binding protein (TBP) is a key component of the

basal factor complex

The binding of RNA polymerase to the promoter of a gene is facilitated by _____

basal factors

The assembly of the basal factor complex at the promoter of a gene is initiated by ____.

binding of the TATA box-binding protein to the promoter

Histone methyltransferases _______.

can act as coactivators or corepressors

Activator proteins often increase transcription through an interaction with ______, proteins that can open local chromatin structure.

coactivators

In eukaryotic cells, certain histone acetyltransferases can act as ______.

coactivators

Small-interfering RNA (siRNA) molecules are produced from

double-stranded RNAs

Which of the following genes encode primary RNAs whose splicing is regulated by the Tra protein?

doublesex (dsx) fruitless (fru)

Activators and repressors bind to _____

enhancers

In yeast, genes can be regulated by upstream activating sequences (UAS). These regulatory elements act in a was similar to _____.

enhancers

DNA-binding domains typically interact with DNA by _____.

fitting within the major groove

Indirect repressors are regulatory proteins that prevent transcription by ______.

interfering with the function of activators

The eIF4e binding protein 1 controls translation in response to nutrient availability in eukaryotic cells. When the cell does not have enough nutrients to grow, this protein

is not phosphorylated

The three classes of small regulatory RNAs that have been identified are

miRNA, siRNA, and piRNA

Which of the following types of RNA are small regulatory RNAs that affect the expression of other genes?

micro-RNAs (miRNAs) small interfering RNAs (siRNAs) Piwi-interacting RNAs (piRNAs)

In Drosophila, sex is determined by the

number of X chromosomes

Splicing of pre-mRNA, altering mRNA stability and controlling the rate of translation are all examples of ______.

posttranscriptional gene regulation

Corepressors can inhibit transcription by ______.

preventing the RNA pol II basal complex from binding to the promoter modifying amino acids in histone tails

Activators can increase RNA synthesis by ______.

recruiting basal factors and RNA polymerase II to promoter sequences

Eukaryotic repressors inhibit transcription by _____.

recruiting corepressor proteins to enhancers

When the TATA box-binding protein binds to a gene's promoter, it _____

recruits other proteins to the promoter

In ribosome profiling, the location of ribosomes along mRNAs are determined based on the fact that _

ribosomes protect from RNA nucleases sequences to which they are bound

In yeast cells, an upstream activating sequence (UAS)usually binds

several copies of a single transcription factor

The enhancer of a eukaryotic gene may interact with _______.

several different activators and repressors that bind to the enhancer with varying affinities

The activation domains of transcription factors promote the activation of RNA polymerase by interacting with __

the basal complex coactivators

Mediator is a protein complex that serves as a bridge between _____.

the basal factor complex and enhancer-binding proteins

Basal transcription factors bind to ______.

the promoter

Which coactivators contain ATPase subunits and use energy from ATP hydrolysis to displace nucleosomes from a promoter?

Chromatin remodeling complexes

Interactions among basal factors, Mediator, and activators bound to distant enhancers are possible because _____.

DNA is flexible and can loop

RNA polymerase II

Genes encoding proteins

RNA polymerase III

Genes encoding tRNAs and some other small RNA molecules

RNA polymerase I

Genes encoding the major ribosomal RNAs (rRNAs)

Which coactivators acetylate amino acid residues within histone tails?

Histone acetyl transferase enzymes

How can gene regulation mechanisms be limited to only a particular gene and not its neighbors?

Insulators between genes organize chromatin and limit enhancer access to promoters.

Each class of small RNA performs its function by forming a ribonucleoprotein complex with a specific member of the Argonaute protein family. What is the role of the small RNA after the complex has formed?

It guides the complex to RNA targets that have perfect or partial complementarity with the small RNA.

If gene regulation occurs at the level of translation such that translation is stopped, what molecules in the pathway will NOT be produced?

Phosphorylated protein Protein

Which of the following are required for the small ribosomal subunit to be able to recognize and bind to an mRNA?

Poly-A binding protein 5' cap Poly-A tail Several initiation factors

Basal factors assist the binding of _______

RNA polymerase II to the promoter of a gene

Select the steps at which gene regulation can occur in eukaryotes.

RNA processing Transcription Posttranslational modification Translation

Select all of these that are posttranscriptional mechanisms that regulate gene expression.

Regulation of mRNA translation Controlling mRNA stability Splicing of pre-mRNA

What type of transcription factor binds to a specific DNA sequence within an enhancer and prevents the initiation of transcription of a gene?

Repressor

Which of the following proteins are considered transcription factors?

Repressors Activators Basal factors

Which type of regulatory RNA molecule may be produced from the processing of RNA from an exogenous source, such as viral RNA

Small-interfering RNA

What protein is the key component of the basal factor complex that assembles on most promoters?

TATA box-binding protein

What is required for activation of transcription of the Sxl gene during embryogenesis in Drosophila?

The presence of two X chromosomes

How do activators interact with other elements at the promoter to increase transcription levels?

They can directly interact with basal factors. They can indirectly interact with basal factors by binding to mediator.

Which of the following are DNA-binding domains that are commonly found in transcription factors?

Zinc finger Helix-turn-helix

Which type of regulatory RNA molecule is produced from the processing of longer double-stranded RNAs?

siRNA

Ribosome profiling is conceptually similar to DNA footprinting in that it identifies locations on mRNA where ribosomes are bound because

those RNA sequences are protected from digestion with RNase