Genetics Chapter 15 and 16
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called ______.
* Control elements * Regulatory sequences * Regulatory elements
Select ways that nucleosomes can change.
* Covalent modifications to the amino-terminal tails of histones * Change in location * Change in histones to variants with specialized roles
Which of the following are true regarding epigenetics?
* Epigenetic changes are transmissible from cell to cell * Epigenetic changes may be transmitted to offspring * Variations are reversible from one generation to the next * Variations of gene expression are unrelated to variations in the DNA base sequence
Enzymes that carry out what functions travel along with RNA polymerase II?
* Histone acetylation * H2B ubiquitination * H3 methylation
Which of the following are examples of epigenetics?
* Localization of histone variants * DNA methylation * Covalent histone modification * Chromatin remodeling
Which of the following represent key functional roles for heterochromatin in eukaryotic cells?
* Preventing viral proliferation * Preventing movement of transposable elements * Silencing genes
What is a motif?
A domain that has a very similar structure in many different proteins
Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin-remodeling complexes?
ATP hydrolysis
What kind of protein is expected to enhance the ability of TFIID to initiate transcription?
Activator proteins
The basic repeating unit of chromatin is the composed of wrapped around an octamer of proteins.
Blank 1: nucleosome Blank 2: DNA Blank 3: histone
What effect can ATP-dependent chromatin remodeling have on transcription?
Both activation and repression
Which enzyme catalyzes the formation of 5-methylcytosine?
DNA methyltransferase
What affect does acetylation have on lysines in core histone protein tails?
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone
Because epigenetics refers to heritable changes in gene expression, all epigenetic changes are examples of transgenerational epigenetic inheritance.
False
How does iron regulatory protein exert its effect on ferritin mRNA?
Iron regulatory protein (IRP) binds to the iron response element (IRE) in the 5' UTR, and thus inhibits ferritin translation.
Which of the following is an example of epigenetic inheritance?
Methylation of DNA that occurs in an oocyte
Which of the following regulates iron assimilation in mammalian cells?
RNA binding proteins
What type of regulatory transcription factor utilizes the strategy depicted in the picture?
Steroid receptor
TFIID binds to the box and helps recruit RNA polymerase II to the core.
TATA, promoter
Activator proteins might help bind to the box.
TFIID, TATA
Which of the following represents de novo methylation?
The methylation of DNA that was previously unmethylated
A transcription factor can have multiple domains.
True
The function of regulatory transcription factors is modulated.
True
The methylation state of DNA is inherited during cell division.
True
Select the organism with the highest amount of DNA methylation.
Vertebrates
Which of the following statements regarding X chromosome inactivation is true?
X chromosome inactivation occurs during embryogenesis in females.
A regulatory transcription factor that enhances the rate of transcription is called a(n) .
activator
Steroid hormones bind regulatory transcription factors called steroid receptors in order to ______.
affect gene transcription
The function of TFIID is to ____
bind to the TATA box and recruit RNA polymerase II to the core promoter.
The CREB protein is a regulatory transcription factor that is activated following an increase in ______.
cAMP
Mediator phosphorylates the -terminus of RNA polymerase II, stimulating progression to the stage of transcription.
carboxyl, elongation
Histone are proteins that bind histones and aid in the assembly of histone octamers.
chaperones
DNA sequences that are analogous to the operator sites found near bacterial promoters are called elements or sequences.
control; regulatory
DNA methylation is the attachment of methyl groups to DNA.
covalent
The methylation of DNA that was previously unmethylated is called methylation
de novo
ATP- remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.
dependent chromatin
Transcription factor proteins contain regions called that have specific functions.
domains
Regulatory elements that inhibit transcription are called silencers and their effect on transcription is called ______ regulation.
down
You are studying a transcription factor that binds to DNA near a gene of interest. You discover that once the transcription factor binds, transcription of your gene of interest becomes undetectable. This is an example of ______.
down regulation
Steroid hormones are synthesized by glands and secreted into the bloodstream, ultimately affecting the transcription or expression of genes in target cells.
endocrine
Activators bind to ______.
enhancers
The variation of gene expression that is not related to the variation of the DNA, is transmissible, and is reversible is described as
epigenetics,
Regions of heterochromatin that vary among different cell types are called heterochromatin.
facultative
Iron response elements (IREs) can be found in the 5'-UTR of mRNA and in the 3'-UTR of mRNA.
ferritin, transferrin receptor
Methylation of the cytosine in both strands is called methylation, and methylation of only one strand is called
full, hemimethylation
The ENCODE Consortium is attempting to list all ______.
functional elements in the human genome
The dimerization of two different proteins leads to a
heterodimer
The function of regulatory transcription factors must be modulated to ensure that genes are turned on ______.
in the correct cell type at the proper time under the appropriate environmental conditions
A sequence found in both ferritin and transferrin receptor mRNAs that is recognized by an RNA-binding protein is called the ______.
iron response element
In order to regulate the translation of both ferritin and transferrin receptor mRNAs, the iron regulatory protein (IRP) binds to the _____ of the mRNAs.
iron response element
Positively charged within core histone proteins can be acetylated by histone
lysines, acetyltransferase
When fully methylated DNA is replicated, it is initially hemimethylated. The hemimethylated DNA is recognized by DNA methyltransferase, which makes it fully methylated. This process is called ______ methylation.
maintenance
If chromatin is in a closed conformation, nucleosome position and histone composition ______.
make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA
The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors is called
mediator
CpG islands near the promoters of tissue-specific genes are often ______
methylated
A domain that has a very similar structure in many different proteins is called a(n)
motif
The phenomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene
regulation
Regulatory transcription factors that prevent transcription from occurring are called
repressors
The cAMP element-binding protein ( protein) is a regulatory transcription factor that is activated in response to signaling molecules that increase cytoplasmic cAMP.
response, CREB
Repressors bind to ______.
silencers
Regulatory transcription factors that respond to steroid hormones are called
steroid receptors
Genes that are highly regulated and may be expressed only in certain cell types are called - genes.
tissue-specific
In helix--helix and helix--helix motifs, an α-helix recognizes a base sequence in the major groove of the DNA.
turn, loop.
The cytosines in CpG islands near housekeeping genes are
unmethylated
When a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains cytosines. This DNA is said to be .
unmethylated, hemimethylated
What is the size of the nucleosome-free region found at the core promoter of active genes?
150 bp
In helix-turn-helix and helix-loop-helix motifs side chains of the α-helix form bonds with nucleotide bases.
Amino acid Hydrogen
What is the name for stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites that are found near gene promoters?
CpG islands
Nucleosomes containing the histone variant , which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone
H2A.Z, H2A
Select the histones for which variants have been identified.
H3 H2A H2B H1
can change in location along a DNA molecule, by replacement of a standard histone with a histone variant, and through covalent modifications on histone tails.
Nucleosomes
Genomic imprinting and X-chromosome inactivation are examples of ______ mechanisms that occur during development.
cis-epigenetic
If an epigenetic change is maintained only at a given site and does not affect the expression of a gene elsewhere in the nucleus, it is a ______ mechanism
cis-epigenetic
Which type of epigenetic mechanism is shown in the image?
cis-epigenetic mechanism
The binding of a regulatory transcription factor to a(n) can stimulate transcription 10- to 1000-fold, which is called regulation.
enhancer; up
DNA methylation, chromatin remodeling, covalent histone modification, and localization of histone variants are all examples of molecular mechanisms that are involved in
epigenetics
The dimerization of two identical proteins results in a
homodimer
Genes that code for proteins that are required in most cells of a multicellular organism are called ______.
housekeeping genes
The central goal of the Encyclopedia of DNA Elements (ENCODE) Consortium is to make a comprehensive list of functional elements in the , including those that control gene expression.
human genome
If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be . If the same sequence of nonmethylated DNA is introduced into a cell, it will be in daughter cells.
methylated, nonmethylated.
An RNA that does not encode a polypeptide is a(n) ______ RNA.
non-coding
Genes that are expressed but do not encode polypeptides produce - RNAs.
non-coding
The core promoter of active genes is found in a(n) -free , which is a segment of DNA that is missing histones.
nucleosome, region
In general CpG islands correlate with active genes, and CpG islands correlate with suppressed genes.
unmethylated, methylated
An enhancer is a DNA element that can be bound to a regulatory transcription factor, which leads to ______.
up regulation
Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone
variants
What DNA sequence is methylated?
5'-CG-3'
If chromatin is in a conformation, transcription may be difficult or impossible.
closed
A protein that increases the rate of transcription but does not directly bind to the DNA is called a
coactivator
Activator proteins often increase transcription through an interaction with ______.
coactivators
Which statement accurately describes the location of iron response elements (IREs) in mRNAs for ferritin and transferrin receptor?
The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.
DNA methyltransferase is an enzyme that attaches a methyl group to the position of the base.
5, cytosine
Gene regulation means that ______.
gene expression can be controlled so that genes can be expressed at high or low levels
Coactivators usually contain a domain that promotes the activation of RNA polymerase.
transactivation
A is a protein that influences the ability of RNA polymerase to transcribe a given gene.
transcription factor
The ATPase subunit of chromatin-remodeling complexes is called DNA
translocase
Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.
* Regulating the binding of the transcriptional complex to the core promoter * Controlling the switch from the initiation to the elongation stage of transcription
The transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with ______.
general transcription factors