BIO Chapter 15 LearnSmart

The function of regulatory transcription factors must be modulated to ensure that genes are turned on in which of the following -in growing cells only -under the appropriate environmental conditions -in the correct cell type -at the proper time -all the time

-under the appropriate conditions -in the correct cell type -at the proper time

Examples of how gene regulation benefits eukaryotic organisms

1. Ability to respond to nutrient changes in nutrient availability 2. The ability to respond to environmental stresses

Steps leading to the activation of the CREB protein

1. An extracellular signaling molecule binds to the plasma membrane receptor 2. A G protein is activated that subsequently activates adenylyl cyclase 3. Adenylyl cyclase catalyzes the synthesis of cAMP 4. cAMP binds to protein kinase A 5. Protein kinase A travels to the nucleus and phosphorylates the CREB protein 6. the CREB protein binds to CBP and RNA polymerase is activated

The pattern of covalent modifications of amino acids on the amino-termini of histones can do what two things?

1. Attract proteins that inhibit transcription 2.Attract chromatin remodeling complexes that alter nucleosome positions to promote transcription

Steps for transcriptional activation of a eukaryotic gene

1. Binding of an activator to an enhancer in the NFR 2. Recruitment of chromatin-remodeling complex and histone-modifying enzyme 3. Recruitment of general transcription factors and RNA pol II to the core promoter, allowing for the formation of a preinitiation complex 4. Eviction or destabilization of histone octamers, allowing RNA pol II to pass and elongation to occur

Common ways that functions of regulatory transcription factors are controlled

1. Binding of small effector molecule 2. Covalent modifications 3. Protein-protein interactions

What are three ways that chromatin remodelers change chromatin structure?

1. Change in nucleosome position 2. Change in the composition of nucleosomes due to exchange of histones 3. Removal of histones from DNA, creating nucleosome free gaps

What are the three ways that nucleosomes can change

1. Covalent modifications to the amino-terminal tails of histones 2. Change in histones to variants with specialized roles 3. Change in location

Enzymes that carry out what functions travel along with RNA polymerase II?

1. H3 methylation 2. H2B ubiquitination 3. Histone acetylation

Strategies used by ENCODE investigators to identify functional elements in the human genome

1. Identify sites where DNAse can cleave DNA 2. Identify sites of histone modification 3. Identify DNA binding sites for transcription factors 4. Map DNA methylation sites 5. Isolate and sequence RNA molecules transcribed by human genome

Repressors inhibit TFIID by

1. Inhibiting ability of TFIID to recruit DNA polymerase II to the core promoter 2. Preventing the binding of TFIID to the TATA box

What are the steps of chromatin immunoprecipitation sequencing (ChIP-Seq)?

1. Living cells are treated with formaldehyde, broken open and treated with micrococcal nuclease 2.Heavy beads attached to antibodies that recognize specific histones are added to the nucleosome mixture 3. The mixture is centrifuged to separate the immunoprecipitated material, crosslinks are reversed and proteases partially digest core histones 4. The remaining DNA is subjected to gel electrophoresis. Fragments of 150 bp are saved 5.Linkers are added to the DNA , then they are PCR amplified and subjected to DNA sequencing. DNA sequences are analyzed

What are the two ways that methylation can affect transcription

1. Methyl-CpG binding proteins recruit other proteins that inhibit transcription 2. The methylation of CpG islands may prevent or enhance the binding of regulatory transcription factors to the promoter region

Common factors that contribute to combinatorial control

1. Regulatory proteins alter the composition or arrangement of nucleosomes in the vicinity of a promoter 2. Activator proteins stimulate the activity of RNA polymerase to initiate transcription 3. Repressor proteins inhibit the ability of RNA polymerase to initiate transcription 4. DNA methylation inhibits transcription 5. Activator and repressor activity is modulated by small effector molecules, protein-protein interactions and covalent modifications

What are the steps of the glucocorticoid hormone and receptor action

1. The glucocorticoid hormone diffuses through the plasma membrane 2. The glucocorticoid hormone binds to glucocorticoid receptors 3. HSP90 is released from the glucocorticoid receptor 4. Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus

Steps at which gene regulation can occur

1. Transcription 2. Translation 3. Posttranslational modification 4. RNA processing

Mapping the locations of nucleosomes in the genomes allows for the determination of ...

1. Where covalent modifications of histones occur 2. Where nucleosomes are located 3. Where histone variants are found

Plants and animals require a greater level of gene regulation than single celled eukaryotes because of

1. multicellularity 2.different developmental stages 3.different tissue types 4.more complex cell structure

Transcription factor

A protein that influences the ability of RNA polymerase to transcribe a given gene

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 transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with

General transcription factors

The function of TFIID is to

Bind to the TATA box and recruit RNA polymerase II to the core promoter

Histone variants that have been identified

H3, H2B, H2A, H1

A histone variant found in the transcribed regions of genes is

H3.3

Which histone variant has not been identified?

H4

According to the ____ ____ hypothesis, the pattern of ____ modification acts like a language or code in specifying alternations in chromatin structure

Histone code; histone

Activator proteins often increase transcription through an interaction with

Coactivators

In general, transcriptional regulation is aimed at

Controlling the initiation of transcription at the promoter

Which enzyme catalyzes the formation of 5-methylcytosine

DNA methyltransferase

A protein called ____ usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around ___

DNAseI; histones

When iron levels in the cytosol rise, iron binds to an iron response element (IRP) so that is dissociates from the mRNA for transferrin receptor, The mRNA is then

Degraded

At the end of many eukaryotic genes, a well positioned nucleosome is followed by an NFR. This arrangement may be important for

Transcriptional termination

In helix-___-helix motifs, and helix-____-helix motifs, an a-helix recognizes a base sequence in the major groove of DNA

Turn;loop

The cAMP response element (CRE) contains _____ of a consensus sequence bound by the CREB protein which has _____

Two copies; Two identical subunits

The cytosines in CpG islands near housekeeping genes are

Unmethylated

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

Select the organism with the highest amount of DNA methylation -Yeast -Vertebrates -Drosophila

Vertebrates

Similar to an a-helix, a ____ finger motif can also recognize the ____ groove of DNA

Zinc;major

Leucine ____ motifs mediate dimerization between two ____

Zipper; proteins

The CREB protein is a regulatory transcription factor that is activated following an increase in

cAMP

Histone ___ are proteins that bind histones and aid in the assembly of histone octamers

chaperones

If a chromatin is in a _____ conformation, transcription may be difficult or impossible

closed

When a methyl-CpG protein associates with a methylated CpG island, it recruits an enzyme called _____ to modify histone proteins which makes it more difficult to remove nucleosomes from the DNA

deacetylase

As RNA polymerase II progresses over the DNA, histone ___ removes acetyl groups behind it, favoring the binding of histones to the ____ to form nucleosomes

deacetylase; DNA

ATP- __________ _____________ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.

dependent chromatin

Steroid hormones are synthesized by the _____ glands and are secreted into the bloodstream, ultimately affecting the transcription or expression of genes in target cells

endocrine

A glucocorticoid response element functions as a

enhancer

Iron response elements (IRE) can be found in the 5'-UTR of ____ mRNA and in the 3'-UTR of _____ ______ mRNA

ferritin; transferrin receptor

The dimerization of two different proteins leads to a

heterodimer

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

In genomic ____, specific genes are ____ during oogenesis or spermatogenesis but not both

imprinting; methylated

Positively charged _____ within core histone proteins can be acetylated by histone ______

lysines; acetyltransferase

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

De novo methylation

methylation of DNA that was previously unmethylated

The placement of ____ at or near promoters often plays a key role in whether a gene is active or inactive

nucleosomes

The function of TFIID is inhibited by ____, which prevent the binding of TFIID to the ____ box

repressors; TATA

Repressors bind to

silencers

Generally, ____ histones are incorporated into nucleosomes during S phase of the cell cycle. Later, histone ___ are added by chromatin-remodeling complexes

standard; variants

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

A process called _____ methylation seems to be the primary mechanism by which DNA in vertebrate and plant cells are methylated

Maintenance

Most common process regarding methylation?

Maintenance methylation

Most eukaryotic genes are regulated by how many factors

Many

Activator proteins stimulate the ability of the ____ to phosphorylate the carboxyl-terminus of RNA pol II, which facilitates the switch between transcriptional initiation and elongation

Mediator

The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors

Mediator

The repressor protein may stop ____ from allowing RNA polymerase to proceed to the _____ phase of transcription

Mediator; elongation

CpG islands near the promoters of tissue-specific genes are often ______.

Methylated

Common types of covalent modifications made to the amino-terminal tails of histones

Methylation, acetylation and Phosphorylation

A domain that has a very similar structure in many different proteins

Motif

The core promoter of active genes is found in a(n) ____-free ___, which is a segment of DNA that is missing histones.

Nucleosome-free region

_____ 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

Transcription can occur more easily when chromatin is in a _____ conformation

Open

Activator proteins stimulate mediator to make what modification to RNA polymerase II?

Phosphorylation

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

Proteins that regulate the rate of transcription of target genes are called ____ transcription factors

Regulatory

Variation in ____ ____ orientation and location makes it difficult to study all the regions of DNA that affect the expression of a given gene

Regulatory element

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

Regulatory elements, regulatory sequences, control elements

T or F? the ChIP Seq method is used on species whose entire genome has been sequenced already?

TRUE

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