week 6 Genetics HW part 2

a change in chromatin confirmation from closed to open often involves the moment of **

**nucleosomes

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

*transcription factor

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

150bp

in somatic cells of female mammals, one of the two X chromosomes becomes a condensed _____ body, where the genes are inactivated

Barr

Stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites and found near gene promoters are called

CpG islands

5-methylcytosine is formed by

DNA methyltransferase

variants have been identified for which of the following histones

H1, H2A, H2B, H3 but not H4

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

TFIID binds to the _____ box and helps recruit RNA polymerase 2 to the core _______

TATA, promoter

which are the most common ways that the functions of regulatory transcription factors are controlled

The binding of small effector molecules, Protein-protein interactions, Covalent modifications.

during embryonic development, many genes undergo ___^^___ changes that enable them to be transcribed or cause them to be permanently repressed

^^epigenetic

variations of gene expression are unrelated to variations in the DNA base sequence, epigenetic changes are transmissible from cell to cell, epigenetic changes may be transmitted to offspring and variations are reversible from one generation to the next

all true regarding epigenetics

the function of TFIID is to

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

first step for transcriptional activation of a eukaryotic gene

binding of an activator to an enhancer in the NFR

what effect can ATP-dependent chromatin remodeling have on transcription

both activation and repression

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

coactivators

activator proteins often increase transcription through an interaction with *

coactivators*

X-chromosome inactivation occurs in _____ cells of _____ mammals

comatic, female

DNA methylation is what of methyl groups to DNA

covalently attachment

what accounts for the variation in coat color in mice

degree of methylation at CpG islands in the TE upstream from the Agouti gene

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

dependent chromatin

are environmental factors that promote epigenetic changes

diet, toxins, temperature

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

enhancer, up

what type of mechanism is responsible for enabling the transcription of muscle-specific genes in an embryonic cell that will eventually give rise to muscle tissue

epigenetic changes

DNA methylation, chromatin remodeling, covalent histone modification and localization of histone variants are all molecular mechanisms that contribute to

epigenetic gene regulation

variation of gene expression that is transmissible and reversible but not related to the variation in the DNA is called

epigenetics

fourth step for transcriptional activation of a eukaryotic gene

eviction or destabilization of histone octamers, allowing RNA polymerase 2 to pass, and elongation to occur

exposure to tobacco smoke has been shown to alter DNA methylation and covalent modifications of specific genes in lung cells, body differences between queen bees and worker bees are caused by dietary differences, flowering and/or seed germination occurs when certain flowering plants are exposed to colder temperatures during the previous winter

examples of how environmental factors may function as epigenetic regulators

gene regulation means that

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

what can be deduced about the effect of DNA methylation levels on expression of the Agouti gene

greater levels of methylation resulted in darker coat color

by changing the histone modification patterns that are recognized by other proteins and by influencing interactions between DNA and histones within nucleosomes are ways that

histone modifications affect the level of transcription

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

the Igf2 gene in mammals is only expressed from the paternal chromosome. this is due to different patterns of DNA methylation during oogenesis and spermatogenesis. Methylation can occur at two different sites:

imprinting control region (ICR) and differentially methylated region (DMR)

region of a chromosome that contains the Igf2 and H19 genes in mammals. ICR refers to _____ ______ region, while DMR stands for _____ _____ region

imprinting control, differentially methylated

proteins called _____-CpG-______ proteins bind methylated sequences and recruit other proteins to the region to ______ transcription

methyl-CpG-binding proteins, inhibit

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 covalent attachment of a -CH3 group to DNA is known as DNA

methylation

the methylation of CpG islands may prevent or enhance the binding of regulatory transcription factors to the promoter region, and methyl-CpG binding proteins recruit other proteins that inhibit transaction are ways that

methylation affect transcription

DNA methylation, chromatin remodeling, covalent histone modification, and localization of histone variants are all molecular mechanisms that contribute to

molecular mechanisms that underlie epigenetic control of gene regulation

the core promoter of active genes is found in a ______-______ ______, which is segment of DNA that is missing histones

nucleosome-free region (NFR)

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

nucleosomes

histone modifications can affect transcription levels by directly influencing interactions within ______, and also by altering the ___ _____

nucleosomes/chromatin, histone code

in eukaryotes, DNA methyltransferase is an enzyme that attaches a methyl group to the _____ position of the _____ base

number 5, cytosine

the function of a regulatory transcription factor can be modulated by covalent modifications, such as the attachment of a

phosphate group

second step for transcriptional activation of a eukaryotic gene

recruitment of a chromatin-remodeling complex and a histone-modifying enzyme

third step for transcriptional activation of a eukaryotic gene

recruitment of general transcription factors and RNA polymerase 2 to the core promoter, allowing the formation of a preinitiation complex

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 phenomenon where gene expression is controlled so that genes can be expressed at high or low levels is called gene

regulation

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 control elements regulatory sequences

DNA sequences that are analogous to the operator sites found near bacterial promoters are called

regulatory or control elements

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

transcription factor

the methylation state of DNA is inherited during cell division

true

in general, ______ CpG islands correlate with active genes, and _____ CpG islands correlate with suppressed genes

unmethylated/hypomethylates, methylated/hypermethylated

an enhancer is a DNA element that is bound by a regulatory transcription factor, which leads to

up regulation