Chapter 16 & 17 reading - Genetics

TFIID binds to the _______1_____ box and helps recruit RNA polymerase II to the core ______2_______

1 - TATA 2 - promoter

The binding of a regulatory transcription factor to a(n) ______1_______ can stimulate transcription 10- to 1000-fold, which is called _____2__ regulation.

1 - enhancer 2 - up

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.

1 - methylated 2 - nonmethylated

Which natural processes would require gene regulation?

1. metabolism 2. response to environmental stress 3. cell division

how many genes does the trp operon contain?

6 total: TrpE, trpD, trpC, trpB, and trpA genes encode enzymes involved in tryptophan biosynthesis trpL gene plays a regulatory role

During attenuation, when trptophan levels are high the __________ stem-loop forms and transcription ____________ the trpL gene. A. 2-3, ends just past B. 3-4, ends just past C. 1-2, continues beyond D. 3-4, continues beyond

B. 3-4, ends just past

On it's chromosome, an E coli cell has the genotype LacI, LacZ, LacY, LacA. It has the F' factor with the genotype LacI, LacZ, LacY, LacA. What is the expected level of expression of the lac operon genes (LacZ, LacY, LacA) in the absence of lactose? A. both lac operons will be expressed B. neither lac operon will be expressed. C. only the chromosomal lac operon will be expressed. D. only the lac operon on the F' factor will be expressed.

B. Neither lac operons will be expressed because lactose is absent

During cell division, from M phase in the mother cell to interphase in the resulting two daughter cells, a chromosome will usually retain the same pattern of _______ and ___________ heterochromatin that was found in the mother cell

Blank 1: constitutive Blank 2: facultative

Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.

Controlling the switch from initiation to the elongation stage of transcription; and regulating the binding of the transcriptional complex to the core promoter

The binding of ________ to a lac repressor causes lac repressor to _____ to the operator site and therby_____ transcription. A. glucose, bind, inhibits B. allolactose, bind, inhbits C. glucose, not bind, increases D. allolactose, not bind, increases

D. allolactose, not bind, increases

Translation can be regulated by: A. translational repressors B. antisense RNA C. attenuation D. both A and B

D. both A (translational repressors) and B (attenuation)

Variants have been identified for which of the following histones? H3 H2A H4 H2B H1

H3, H2A, H2B, H1 but NOT H4

CAP site (in lac operon)

Is a DNA squence recognized by an activator protien called catabolite activator protien (CAP)

is trpR gene part of the trp operon? what does it do?

No, it encodes the trp repressor protien

where are the three operator sites of the lac operon located?

O1 is slightly downstream from the promoter O2 is located farther downstream in the lacZ coding sequence O3 is located slightly upstream from the promoter

Which of the following represent key functional roles for heterochromatin in eukaryotic cells?

Preventing movement of transposable elements Silencing genes Preventing viral proliferation

Which of these are true regarding epigenetics?

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

Interphase -Most chromosomal regions are composed of euchromatin. M phase-Euchromatic regions condense into constitutive and facultative heterochromatin. M phase through interphase in two daughter cells - Constitutive and facultative heterochromatin regions retain the same pattern observed in mother cell.

X

is a small effector molecule that binds to a repressor protien, thereby causing the protien to bind to the DNA. What is this molecule?

a corepressor

operon

a group of two or more genes together under the control of a single promoter

lac repressor

a protien that is important for the regulation of the lac operon. This repressor is a homotetramer, a protien composed of four identical subunits. The amount of lac repressor made is approx. 10 molecules per cell

trans-acting factor

a regulatory protein that binds to a regulatory element in the DNA and exerts a trans effect

Cis-acting element

a sequence of DNA, such as a regulatory element, that exerts a cis-effect

gene regulation

ability of an organism to control which genes are transcribed in response to the environment

DNA methylation is the ________________ attachment of methyl groups to DNA.

covalent

posttranslational covalent modification

the covalent modification of the structure of a protien after it has been synthesized via ribosomes

Enzyme adaptation

the phenomenon in which a particular enzyme appears within a living cell after the cell has been exposed to the substrate for that enzyme

diauxic growth

the sequential use of two sugars by a bacterium

Feedback inhibition

the synthesis of many cellular molecules such as amino acids, vitamins, and nucleotides occurs via the action of a series of enzymes that convert precursor molecules to particular products. During feedback inhibition, the final product in a metabolic pathway inhibits an enzyme that acts early in the pathway

catabolite repression

this form of transcriptional regulation is influenced by the presence of glucose, which is a catabolite - a substance that is broken down inside the cell

In eukaryotic cells, which processes are prevented by heterochromatin formation? Multiple select question.

transcription viral proliferation transposable element movement

attenuation

transcription begins but is stopped prematurely before most of the trp operon is transcribed

A protein that influences the ability of RNA polymerase to transcribe DNA into RNA is called a(n)______________

transcription factor

How do transcription factors contribute to epigenetic modification?

transcription factors recruit chromatin modifying protiens, such as DNA methyltransferase

Riboswitch can regulate:

transcription, translation, RNA stability, or splicing

merozygote

A partially diploid cell; a strain of bacteria containing F' factor genes

When tryptophan binds to trp repressor this causes trp repressor to____________ to the trp operator and ___________ transcription. A. bind, inhibit B. not bind, inhibit C. bind, activate D. not bind, activate

A. bind, inhibit

For a riboswitch that controls transcription the binding of a small molecule such as TPP controls whether the mRNA A. has an anti-terminator or terminator stem-loop B. has a shine-Dalgarno antisequestor or the shine-Dalgarno sequence within a stem-loop C. is degraded from its 5' end D. has both a and b

A. has an antiterminator or terminator stem- loop

An enhancer is a DNA element that is bound by a regulatory transcription factor, which leads to ______. A. Up regulation B. transcriptional repression C. DNA replication D. down regulation

A. up regulation

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

A repressor is a __________ that ________ transcription. A. small effector molecule, inhibits B. small effector molecule, enhances C. regulatory protien, inhibits D. regulatory protien, enhances

C. a repressor is a regulatory protien that inhibits transcription

Lysine residues on core histone proteins can be acetylated by enzymes called histone ____________.

acetyltransferase

Genes that are regulated by inducers are called:

inducible genes

regulation by an activator is considered to be:

positive control

constitutive genes

unregulated genes

What is the size of the nucleosome-free region found at the core promoter of active genes? A. 150 base pairs B. 15 base pairs C. 1,500 base pairs D. 15,000 base pairs

A. 150 base pairs

antisense RNA

an RNA strand that is complementary to a strand of mRNA. (the mRNA strand has the same sequence as the DNA sense strand

binds to an activator protien and prevents if from binding to the DNA

an inhibitor

polycistonic mRNA

an mRNA that contains the sequences of two or more genes

In the thi operon in B. subtilis, when levels of TPP are low, the 5' end of the mRNA forms a stem-loop structure called a(n) _________ that allows transcription to continue.

antiterminator

Which of the following combinations would cause the rate of transcription to increase? A. a activator plus an inducer B. a repressor plus a corepressor C. an activator plus an inhibitor D. none of the above would increase the rate of transcription

A. a activator plus an inducer

Operons involved with the biosynthesis of molecules, such as amino acids are most likely to be regulated in which of the following ways? A. the product of the biosynthetic pathway represses transcription B. the product of the biosynthetic pathway activates transcription C. A precursor of the biosynthetic pathway represses transcription D. A precursor of the biosynthetic pathway activates transcription

A. the product of the biosynthetic pathway represses transcription

What is an Operon? A. a site in the DNA where a regulatory protien binds B. a group of genes under the control of a single promoter C. an mRNA that encodes several genes D. all of the above are true of an operon

B. a group of genes under the control of a single promoter

(thiamin example) When TPP levels are low, TPP is not bound to the aptamer domain, and the secondary expression platform has a stem loop called:

an antiterminator, and prevents the formation of the terminator stem-loop. under these conditions, transcription of the entire the operon occurs. In this way, the bacterium is able to make more TPP which is in short supply

allosteric enzyme

an enzyme that contains two binding sites: a catalytic site (responsible for binding of the substrate and its conversion to intermediate) and a regulatory site (binds the final product of the metabolic pathway). When bound to the regulatory site the final product causes a conformational change that inhibits the catalytic ability of enzyme 1

To facilitate transcription an operon is flanked by a ___________that signals the beginning of transcription, and a ___________ that signals the end of transcription

promoter, terminator

allosteric regulation

allosteric protiens have at least two binding sites. the effector molecule binds to the protien's allosteric site, which is a site other than the protien's active site. In the case of lac repressor, the active site is the part of the protien that binds to the DNA

small effector molecule that causes the rate of transcription to increase. SOme bind to a repressor protien to prevent it from binding to the DNA whereas others bind to an activator protien and cause it to bind to the DNA. Both cases cause the transcription rate to be increased. What is this molecule?

an inducer

(gram-positive bacteria example) when TPP levels are high TPP ___ to the aptamer domain and causes a switch in the secondary structure of the expression platform. The expression platform that contains the ____ sequence and the start codon. The formation of this stem-loop sequesters the Shine-Dalgarno sequence, thereby preventing ______. This blocks the translation of the enzymes that are needed to make more TPP.

binds shine-dalgarno ribosomal binding

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

both activation and repression

Many epigenetic modifications are programmed changes that occur during developmental stages such as ______ or __________ .

gametogenesis embryogenesis

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; and under the appropriate environmental conditions

operator site

is a sequence of bases that provides a binding site for a repressor protien

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

methylation

The regulatory transcription factors that respond to glucocorticoid hormones are called glucocorticoid ___________

receptors

activator

regulatory protien that binds to DNA and increases rate of transcription

repressor

regulatory protien that binds to DNA and inhibits transcription

genes that are regulated by corepressors or inhibitors are termed:

repressible genes

Anabolic enzymes are usually encoded by ______ operons, and ______ operons usually encode catabolic enzymes.

repressible; inducible

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 process that uses the energy of ATP hydrolysis to change the position or composition of nucleosomes is called ATP- ____________________________ remodeling

dependent chromatin

(gram-positive bacteria example) when TPP levels are low, TPP _________ bind to the aptamer domain at the ___ end of the mRNA and the expression platform adopts a secondary structure that contains a stem-loop called the ________ antisequestor. When this stem-loop forms the _________ sequence is accessible which allows the mRNA to bind to the ribosome. Therefore the mRNA is translated when TPP is in short supply.

does not 5' shine-dalgarno shine-dalgarno

attenuator sequence

downstream of trpL gene; When attenuation occurs, the mRNA from the trp operon is made as a short piece that terminates at the attenuator sequence

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

epigenetics

Regions of heterochromatin that vary among different cell types are called _______________ heterochromatin.

facultative

In eukaryotes, DNA methyltransferase is an enzyme that attaches a methyl group to the ___________ position of the ________ base.

fifth cytosine

trans-effect

form of gene regulation that can occur even though two DNA segments are not physically adjacent

posttranslational regulation

functional control of protiens that are already present in the cell rather than regulation of transcription or translation

What are the steps in a simplified model for transcriptional activation of a eukaryotic gene in order, with 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 polymerase II to the core promoter, allowing the formation of the preinitiation complex 4. eviction or destabilization of histone octamers, allowing RNA polymerase II to pass and elongation to occur

transcription regulation by a repressor is termed:

negative control

Besides DNA and histone proteins, __________-___________ RNAs are a critical component of chromatin.

non-coding

osmoregulation

the ability of a cell to control the amount of water inside it.

(thiamin example) When TPP levels are high, TPP binds to the aptamer domain and causes a switch in the secondary structure of the expression platform. What sort of stem-loop forms in this case?

the terminator stem-loop which will abruptly stop transcription and inhibit the production of the enzymes that are needed to make more TPP

An example of a posttranslational covalent modification that may affect protein function is: A. phosphorylation B. acetylation C. methylation D. any of the above can affect protein function

D. any of the above can affect protein function

When an E. Coli cell is exposed to glucose, how does this affect the regulation of the lac operon via CAP? A. cAMP binds to CAP and transcription is increased B. cAMP binds to CAP and transcription is decreased C. cAMP does not bind to CAP and transcription is increased. D. cAMP does not bind to CAP and transcription is decreased

D. cAMP does not bind to CAP and transcription is decreased

Which of these are molecular mechanisms that underlie epigenetic control of gene expression?

DNA methylation. Chromatin remodeling. Covalent Histone modification. localization of histone variants

Inducible operons usually encode ______ enzymes, and repressible operons usually encode ______ enzymes.

catabolic; anabolic

Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.

controlling the switch from the initiation to the elongation stage of transcription regulating the binding of the transcriptional complex to the core promoter

Which of these are molecular mechanisms that underlie epigenetic control of gene expression?

covalent histone modification chromatin remodeling localization of histone variants DNA methylation

A fibrous layer of proteins lining the inner nuclear membrane of eukaryotic cells is called the ______. Multiple choice question.

nuclear lamina

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

Whether a gene is active or inactive often depends on the placement of _________________ at or near its promoter region.

nucleosomes

The binding of the micF RNA to the ompF mRNA prevents _____________ from being translated

ompF mRNA

Genetic regulatory proteins that respond to small effector molecules have two functional domains

one domain site where the protien binds to the DNA the other domain is the binding site for the effector molecule

cyclic-AMP (cAMP)

small effector molecule, which is produced from ATP via an enzyme known as adenmyly cyclase

True or false: The methylation state of DNA is inherited during cell division.

true

A change in chromatin confirmation from closed to open often involves the movement of ______. A. nucleosomes B. promoters C. helicases D. genes

A. nucleosomes