Exam III Review control of transcription initiation chapter 16

Question 1

Promoters

Answer 1

Regulatory regions for genes transcribed in a cell type specific manner, always very close to the genes protein coding region. Upstream.

Question 2

Tata box

Answer 2

Part of the promoter upstream of the transcription initiation site binding of RNA polymerase occurs here, An initiation box consisting of roughly 7 nucleotide sequence T a T a (a or T) a (A or T), Allows basal level of transcription

Question 3

Enhancer

Answer 3

A regulatory site that can be quite distant – up to 10,000’s nucleotides away from the promoter, can augment or repress Basal levels of transcription. A single _______ may have multiple binding sites for different transcription factors. Maybe located either five prime or three prime to the transcription start site

Question 4

Sequence specific DNA binding proteins that influence transcription (basal factors, activators, or repressors)

Answer 4

Transcription factor

Question 5

Tata box binding protein, assists in the binding of RNA polymerase II to the promoter

Answer 5

Basal transcription factor TBP

Question 6

Tata box binding protein associated factor recruited by TBP, assists in the binding of RNA polymerase two

Answer 6

Basil transcription factor TAF (Tbp – associated factors)

Question 7

Transcription factors that bind to enhancers to increase transcriptional activity by interacting directly or indirectly with Basal factors at the promoter. Responsible for much of the variation in levels of transcription of different genes.

Answer 7

Activators

Question 8

The structural domain with in an activator protein which mediates binding to enhancer DNA, which interact with other proteins to activate transcription

Answer 8

DNA – binding domain

Question 9

DNA-binding motifs found in activators

Answer 9

DNA binding domain helix loop helix

Question 10

DNA-binding structure found mainly in eukaryotic activator proteins

Answer 10

Zinc fingers

Question 11

DNA-binding structure found mainly in prokaryotes Activator proteins for example the lack repressor

Answer 11

Helix turn helix

Question 12

Part of an activator that binds to DNA, binds to either identical (homodimer) or non-identical heterodimer subunits

Answer 12

Dimerization domain

Question 13

A helix with Leucines at regular intervals, June – June homodimers May interact, June – fos heterodimers may interact. Both are motifs found in activator proteins

Answer 13

Leucine zipper dimerization domain

Question 14

Eukaryotic transcription factors that bind specific DNA sites near a gene and prevent the initiation of transcription of the gene by recruiting call repressor proteins that either prevent the RNA polymerase II complex from finding the promoter or modify histones to close chromatin structure

Answer 14

Repressor

Question 15

Indirect repression. A protein can bind the activation domain of an activator bound to an enhancer and thereby prevent the activator from functioning

Answer 15

Quenching

Question 16

Part of the activator protein that binds to other proteins

Answer 16

Activation domain

Question 17

Competition due to overlaping binding sites, quenching, (repressor blocks activation domain) cytoplasmic sequestration, heterodimerization

Answer 17

Ways and indirect repressor can interfere with the function of an activator

Question 18

DNA sequences located between a promoter and an enhancer that block the enhancer from activating transcription from that promoter

Answer 18

Insulators

Question 19

Binds insulators and facilitates the formation of DNA loops

Answer 19

Ccctc binding factor CTCF

Question 20

One chromatin is isolated from the cell nuclei. Two DNA and proteins are chemically cross-linked wig formaldehyde. Three DNA is fragmented by sonication. Four antibody specific to the protein of interest is used. Five DNA to which protein was bound is purified and sequenced.

Answer 20

Chromatin immunoprecipitation-sequencing Chip-seq)

Question 21

Beyond genetics specifically beyond the nucleotide sequence of DNA (modifications)

Answer 21

Epigenetics

Question 22

A methyl group is added to a cytosine base that is followed by a guanine by DNA methyl transferases. Control of transcription.

Answer 22

DNA methylation

Question 23

Regions with a high concentration of CPG dinucleotides

Answer 23

CPG islands

Question 24

When a cpg island near a promoter is unmethylated, the gene is transcriptionally active. In the absence of a transcriptional activator, the CPG Island becomes methylated. Methyl CPG binding proteins bind and close the chromatin structure.

Answer 24

DNA methylation at cpg islands silences gene expression

Question 25

Caused by a loss of function mutations in meCPg (methyl CPG binding protein) gene on the X chromosome.

Answer 25

Rhett syndrome

Question 26

Long term repression through DNA methylation

Answer 26

Silencing

Question 27

Expression of an allele depends on the parent that transmits it. Methylation at imprinting control regions ICRs silences Jean expression.

Answer 27

Genomic imprinting

Question 28

Paternal allele is silence, maternal allele is expressed

Answer 28

Paternally imprinted

Question 29

Maternal allele is silenced, paternal allele is expressed

Answer 29

Maternally imprinted

Question 30

Deletion on a chromosome 15 passed from mother

Answer 30

Angelman syndrome

Question 31

Deletion on chromosome 15 passed from father, never feel full

Answer 31

Prater – Willi syndrome

Question 32

In IGF-II transcriptional repressor binds to unmethylated DNA and prevents transcription

Answer 32

CTCF

Question 33

Imprinting only occurs in placental mammals. Maternally imprinted paternally express genes like IGfr II promote prenatal growth while paternally imprinted maternally express genes like IGFr2 restrict prenatal growth

Answer 33

Parental conflict hypothesis

Question 34

At the level of RNA, splicing, stability, and localization (where it gets to). At the level of protein, synthesis, stability, localization, and modifications.

Answer 34

Post transcriptional regulation can occur at many steps

Question 35

a class of small, RNAs They play an important regulatory role by targeting specific mRNAs for degradation or translation repression. Negative regulators of target mRNAs resulting in the destruction of these mRNAs or preventing them from being translated

Answer 35

Micro RNA’s

Question 36

Ribonuclease enzyme in the nucleus that processes/crops pre-miRNAs (double-stranded stem loops)

Answer 36

Drosha

Question 37

Ribonuclease enzyme that cuts loop in the cytoplasm

Answer 37

Dicer

Question 38

MiRNAs become incorporated into ribonucleoprotein complexes that contain particular member of the Argonaut protein family. Becomes functional and highly specific by eliminating the MiRNA strand that is partially complementary to the MiRNA that will serve as the guide.

Answer 38

MiRISC’s

Question 39

After transcription pri-mirna are recognized by Drosha in the nucleus which crops out pre-MiRNA stem loop structures. When transported into the cytoplasm pre MiRNA is diced by dicer. MiRNA MiRNA duplex is degraded and picked up by risc. Risc degrades the strand that is complementary to the MiRNA that will serve as the guide to RIsC (RNA induced silencing complex).

Answer 39

MiRNA processing

Question 40

Rna induced silencing complex. Binding to messenger RNA results in cleavage.

Answer 40

RISC

Question 41

RNA polymerases one, two, and three.

Answer 41

One, transcribes genes that encode the major RNA components of ribosomes (rRNAs). Two, transcribes genes that encode all proteins. Three, transcribes Genes that encode the transfer RNAs as well as certain other small RNA molecules

Question 42

Post transcriptional processing

Answer 42

Splicing, polyadenylation, 5’ cap addition

Question 43

Sqcchd

Answer 43

Sequestration, quenching, competition, chromatin, direct

Indirect repression. Repressor vs activator

Question 44

Three ways eukaryotes regulate their genes

Answer 44

Three are in a polymerases. Post transcriptional regulation. Imprinting.

Question 45

Post transcriptional regulation. RNA. SLs.

Answer 45

Splicing, localization, stability.

Question 46

Post transcriptional regulation. Protein. SSLM.

Answer 46

Synthesis, stability, localization, modifications.

Question 47

Post transcriptional regulation. RNA. SLs.

Answer 47

Splicing, localization, stability.

Question 48

Post transcriptional regulation. Protein. SSLM.

Answer 48

Synthesis, stability, localization, modifications.

Question 49

Transcription factors that bind to enhancers to increase transcriptional activity by interacting directly or indirectly with Basal factors at the promoter. Responsible for much of the variation in levels of transcription of different genes.

Answer 49

Activator