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Biochem exam 3 > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

1
Q

What is LRP5?

A

LDL receptor-related protein 5

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2
Q

What is BMP4?

A

bone morphogenetic protein 4

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3
Q

What is IRF6?

A

interferon-regulatory factor 6

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4
Q

What is GRHL3?

A

grainyhead-like 3

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5
Q

What is AMOT?

A

angiomotin

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6
Q

What is a gene?

A

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

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7
Q

What is the central dogma?

A

DNA>RNA> protein

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8
Q

Are all genes expressed in all cell types?

A

no
-only housekeeping genes are on in every cell

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9
Q

Why is gene regulation important?

A

-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

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10
Q

What are promoters and transcriptional start sites?

A

TATA box- helps position RNA polymerase

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11
Q

What are enhancers?

A

function far from transcription start site but enhance gene expression

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12
Q

What are silencer/repressor elements?

A

opposite of enhancer function

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13
Q

What are response elements?

A

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

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14
Q

What are insulators? (boundary elements)

A

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

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15
Q

What are CpG islands?

A

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

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16
Q

What are the general requirements of gene expression control?

A

core transcriptional machinery (ex: RNA polymerase)

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17
Q

What are the specific requirements of gene expression control?

A

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

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18
Q

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

A

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

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19
Q

How does DNA exist in the cell?

A

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

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20
Q

What are histones?

A

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

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21
Q

How many times does DNA wind around histones?

A

1.65 times

22
Q

disruption of histones=

A

disruption of gene expression

23
Q

What are the modifications of histone tails possible?

A

-acetylation
-methlyation
-phosphorylation

*controls TF interaction

24
Q

what does histone methylation do to gene expression?

A

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

25
Q

What are characteristics of DNA?

A

-right handed helix
-minor and major grooves

26
Q

What is helix-loop-helix motif?

A

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

27
Q

What are Zinc-finger motifs?

A

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

28
Q

What is a helix-turn-helix motif?

A

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

29
Q

What is a leucine zipper motif?

A

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

30
Q

Where does the alpha helix bind to DNA?

A

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

31
Q

What does a leucine zipper do?

A

promote dimerization and DNA binding

32
Q

What are nuclear hormone receptors?

A

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

33
Q

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

A

hydrogen atoms and methyl groups

34
Q

Class I nuclear hormone receptors

A

ligand bound in cytosol –> complex moves to nucleus

35
Q

Class II nuclear hormone receptors

A

ligand enter nucleus to bind receptors on DNA

36
Q

Do transcription factors act alone?

A

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

37
Q

What do promoters do?

A

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

38
Q

Are enhancers/silencers always close to the start site?

A

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

39
Q

What is the TATA box?

A

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

40
Q

What is the INR?

A

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

41
Q

What is the DPE?

A

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

42
Q

What is the BRE?

A

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

43
Q

When are chromosomes less packed?

A

when undergoing mitosis

44
Q

What allows enhancers and promoters to come together?

A

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

45
Q

Does transcriptional activation occur at one spot at a time?

A

no, occurs at hundreds of genes at once

46
Q

What does the gene expression program dictate?

A

cellular response and alters cellular and tissue phenotype

47
Q

Is gene expression controlled only by tissue type?

A

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

48
Q

What do mutations in Wnt10a cause?

A

oligodontia/hypodontia

49
Q

What do mutations in Wnt9b cause?

A

cleft lip/palate

50
Q

Is gene expression regulated at one level?

A

no, there are many levels of regulation for gene expression

Biochem exam 3 (10 decks)

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