BIO 140 Ch 15. Connect Concepts

Click and drag on elements in order. Place these steps in a simplified model for transcriptional activation of a eukaryotic gene in order from first to last, putting the first step at the top.

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

What is the size of the nucleosome-free region found at the core promoter of active genes?

150 bp

DNA methyltransferase is an enzyme that attaches a methyl group to the _________ position of the _______ base

5; cytosine

The function of TFIID is to ________

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

A protein that increases the rate of transcription but does not directly bind to the DNA is called a __________

Coactivators

Which enzyme catalyzes the formation of 5-methylcytosine?

DNA methyltransferase

Select the histones for which variants have been identified

H1, H2A, H2B, H3

Nucleosomes containing the histone variant ____________, which are usually found at the +1 nucleosome, are thought to be more easily removed from DNA the DNA than those containing the standard histone __________________

H2A Z; H2A

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 core promoter of active genes is found in a(n) ________________-free __________, which is a segment of DNA that is missing histones

Nucleosome; region

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

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

T/F: A transcription factor can have multiple domains

True

T/F: The function of regulatory transcription factors is modulated.

True

T/F: The methylation state of DNA is inherited during cell division

True

An enhancer is a DNA element that can be bound to a regulatory transcription factor, which leads to ______

Up regulation

Select the organism with the highest amount of DNA methylation

Vertebrates

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

cAMP

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

closed

Activator proteins often increase transcription through an interaction with ________.

coactivator

DNA methylation is the ________ attachment of methyl groups to DNA

covalent

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

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 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 elemeny

Positively charged ________ within core histone proteins can be acetylate 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

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

The binding of a regulatory transcription factor to a(n) _________ can stimulate transcription 10- to 1000- fold, which is called _______________ regulation

regulatory element; up

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

A __________ ____________ is a protein that influences the ability of RNA polymerase to transcribe a given gene.

transcription factor

In general _________ CpG islands correlate with active genes, and _________ CpG islands correlate with suppressed genes

unmethylated; methylated

What effect can ATP-dependent chromatin remodeling have on transcription?

Both activation and repression

Select ways that nucleosomes can change

Change in location; change in histones to variants with specialized roles; & Covalent modifications to the amino-terminal tails of histones

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

A sequence found in both ferritin and transferrin receptor mRNAs that is recognized by an RNA-binding protein is called the __________

Iron response element

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

The function of regulatory transcription factors must be modulated to ensure that genes are turned on ________

Under the appropriate environmental conditions, in the correct cell type, and at the proper time

The ENCODE Consortium is attempting to list all ________

functional elements in the human genome

Gene regulation means that __________________

gene expression can be controlled so that genes can be expressed at high or low levels

Regulatory transcription factors that respond to steroid hormones are called __________

steroid receptor

Most histone genes encode standard histone proteins. These proteins are called histone _________.

variants

______ 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