Regulation of Gene Expression

Question 1

What is LRP5?

Answer 1

LDL receptor-related protein 5

Question 2

What is BMP4?

Answer 2

bone morphogenetic protein 4

Question 3

What is IRF6?

Answer 3

interferon-regulatory factor 6

Question 4

What is GRHL3?

Answer 4

grainyhead-like 3

Question 5

What is AMOT?

Answer 5

angiomotin

Question 6

What is a gene?

Answer 6

a segment of DNA that is transcribed into RNA
-associated regions that control how, when, where, and in what amount RNA is transcribed

Question 7

What is the central dogma?

Answer 7

DNA>RNA> protein

Question 8

Are all genes expressed in all cell types?

Answer 8

no
-only housekeeping genes are on in every cell

Question 9

Why is gene regulation important?

Answer 9

-determines how a cell can take on specialized functions
-determines how a cell responds to environmental change or external stimuli
-determine maintenance of tissue homeostasis
-morphogenesis (growth & shape change)
-cell communication (response to signals from neighboring cells)
-evolutionary adaptation (changes in gene regulation can lead to new traits)
-immune responses

Question 10

What are promoters and transcriptional start sites?

Answer 10

TATA box- helps position RNA polymerase

Question 11

What are enhancers?

Answer 11

function far from transcription start site but enhance gene expression

Question 12

What are silencer/repressor elements?

Answer 12

opposite of enhancer function

Question 13

What are response elements?

Answer 13

specific sequences within enhancers and silencers that respond to signaling pathways and environmental cues

Question 14

What are insulators? (boundary elements)

Answer 14

act as barriers to restrict action of enhancers/silencers to particular genes

Question 15

What are CpG islands?

Answer 15

stretches of DNA sequences that have a content of CpG dinucleotides (cytosine followed by guanine)
cytosine bases in these islands are often targeted for methylation (type of epigenetic modification)
-control gene expression

Question 16

What are the general requirements of gene expression control?

Answer 16

core transcriptional machinery (ex: RNA polymerase)

Question 17

What are the specific requirements of gene expression control?

Answer 17

-intracellular hormone-receptor complexes
-intracellular second messenger
-gene specific transcription factors
-gene regulatory sequences

Question 18

What are some examples of proteins that are involved with gene expression?

Answer 18

-activation/coactivator
-repressor/ corepressors
-mediators and DNA binding proteins
-chromatin remodeling proteins
-histone acetylase/deactelyase
-histone methylation
-DNA methylation

Question 19

How does DNA exist in the cell?

Answer 19

it exists as a highly condensed nucleosome form with numerous associated proteins

Question 20

What are histones?

Answer 20

highly basic proteins that bind to DNA
-five families: H1/H5 (linker), H2-H4 (core)
-abundant in arginine and lysine amino acids
-act as dynamic spools for DNA, creating nucleosomes
-control transcription factors access to gene regulatory elements

Question 21

How many times does DNA wind around histones?

Answer 21

1.65 times

Question 22

disruption of histones=

Answer 22

disruption of gene expression

Question 23

What are the modifications of histone tails possible?

Answer 23

-acetylation
-methlyation
-phosphorylation

*controls TF interaction

Question 24

what does histone methylation do to gene expression?

Answer 24

blocks the association of enzymes and blocks the activation of gene expression

Question 25

What are characteristics of DNA?

Answer 25

-right handed helix -minor and major grooves

Question 26

What is helix-loop-helix motif?

Answer 26

common in transcription factors and consists of alpha helices bound by a looping stretch of amino acids

Question 27

What are Zinc-finger motifs?

Answer 27

bind to DNA and have zinc metal ions associated with the protein -some have an alpha helix plus beta sheet structure, others have a more helix-turn-helix structural motif -can be monomers or dimers

Question 28

What is a helix-turn-helix motif?

Answer 28

DNA binding motif consisting of two alpha helices joined by a short stretch of amino acids -homeobox proteins

Question 29

What is a leucine zipper motif?

Answer 29

two proteins each with an alpha helix formed a Y shaped coiled-coil structure -results in both protein and DNA binding

Question 30

Where does the alpha helix bind to DNA?

Answer 30

major groove -residues in recognition alpha helix bond with certain bases in the DNA -HTH proteins function as dimers, so require optimal DNA sequence in both major groove

Question 31

What does a leucine zipper do?

Answer 31

promote dimerization and DNA binding

Question 32

What are nuclear hormone receptors?

Answer 32

important class of transcription factors activated by ligand -endogenous hormones, sterols, vitamin A, vitamin D, and xenobiotics -often contain two zinc fingers, that recognize a bipartite sequence -ligand binding can stabilize/initiate interaction with other TFs

Question 33

what do protein motifs look for in minor and major grooves to know where to bind?

Answer 33

hydrogen atoms and methyl groups

Question 34

Class I nuclear hormone receptors

Answer 34

ligand bound in cytosol --> complex moves to nucleus

Question 35

Class II nuclear hormone receptors

Answer 35

ligand enter nucleus to bind receptors on DNA

Question 36

Do transcription factors act alone?

Answer 36

no -partners enhance stability of interaction with DNA -co-operative binding requires nearby recognition sites for each TF

Question 37

What do promoters do?

Answer 37

help to define the transcription start site -position the RNA polymerase

Question 38

Are enhancers/silencers always close to the start site?

Answer 38

no, they can be 5' of promoter, 3' of flanking regions, and introns

Question 39

What is the TATA box?

Answer 39

located 25-30 bp of 5' start site, binds TBP subunit TFIID

Question 40

What is the INR?

Answer 40

initiator -contains the start site of transcription for RNA polymerase II genes -bind TFIID

Question 41

What is the DPE?

Answer 41

downstream promoter element -located at +30 of the start site, binds TFIID

Question 42

What is the BRE?

Answer 42

TFIIB-recognition element -located at -35 of the start site, binds TFIIB

Question 43

When are chromosomes less packed?

Answer 43

when undergoing mitosis

Question 44

What allows enhancers and promoters to come together?

Answer 44

extracellular stimuli of cells expressing appropriate transcription factors -assembly of transcriptional complexes

Question 45

Does transcriptional activation occur at one spot at a time?

Answer 45

no, occurs at hundreds of genes at once

Question 46

What does the gene expression program dictate?

Answer 46

cellular response and alters cellular and tissue phenotype

Question 47

Is gene expression controlled only by tissue type?

Answer 47

no, it is also controlled by timing -if genes are on at wrong times, there can adverse affects

Question 48

What do mutations in Wnt10a cause?

Answer 48

oligodontia/hypodontia

Question 49

What do mutations in Wnt9b cause?

Answer 49

cleft lip/palate

Question 50

Is gene expression regulated at one level?

Answer 50

no, there are many levels of regulation for gene expression