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BIO 214 > Control of Gene Expression > Flashcards

Control of Gene Expression Flashcards

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Biology 101 flashcards
1
Q

Controlling gene expression can often be achieved by controlling _______ _______

A

transcription initiation

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2
Q

_______ _______ bind to DNA, modulating the binding of RNA polymerase to the promoter

A

Regulatory proteins

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3
Q

_______ organisms regulate gene expression in responds to their environment

A

Prokaryotic

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4
Q

_______ cells regulate gene expression to maintain a constant internal environment (_______ ) in the organism

A

Eukaryotic, homeostasis

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5
Q

Regulatory proteins gain access to the bases of DNA at the _______ _______

A

major groove

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6
Q

Regulatory proteins possess DNA-binding _______

A

motifs

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7
Q

Regulatory proteins either block transcription by preventing _______ _______ to bind, or stimulate transcription by facilitating it to bind to the _______

A

RNA polymerase, promoter

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8
Q

Within the major groove, nucleotides’ _______ _______ donors and acceptors are accessible. There is a unique pattern of accessibility for each base pair combination which enables _______ to read the sequence without _______ DNA

A

hydrogen bond, proteins, unwinding

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9
Q

DNA-binding _______ are regions of _______ proteins which bind to DNA

A

motifs, regulatory

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10
Q

The _______-_______-_______ motif is two α-helical segments linked by a nonhelical segment. The _______ is a special class of this and is critical in Eukaryotic development

A

Helix-turn-helix, Homeodomain

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11
Q

The _______ _______ motif has several forms, and uses zinc atoms to coordinate DNA binding

A

Zinc finger

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12
Q

The _______ _______ motif is a dimerization motif in which a region in one subunit interacts with a similar region on another subunit forming a zipper-like connection

A

Leucine zipper

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13
Q

In Prokaryotic regulation, Transcription inititiation can be _______ or _______ controlled

A

positively, negatively

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14
Q

_______ control of prokaryotic transcription initiation increases frequency. _______ enhance binding of RNA polymerase to the _______

A

Positive, Activators, promoter

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15
Q

_______ control of Prokaryotic transcription initiation decreases frequency. _______ bind to regulatory sites on DNA called _______ that prevent or decrease initiation frequency

A

Negative, Repressors, operators

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16
Q

_______ molecules can act on both repressors and activators

A

Effector

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17
Q

Prokaryotic cells often respond to their _______ by changes in gene expression. Genes involved in the same metabolic pathway are organized in _______.

A

environment, operons

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18
Q

_______ occurs when the presence of a substrate (a specific substance) triggers the production of enzymes needed to produce it

A

Induction

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19
Q

_______ means the cell is capable of making an enzyme but doesn’t

A

Repression

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20
Q

The _______ _______ encodes proteins necessary for the use of lactose as an energy source

A

lac operon

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21
Q

β-galactosidase is known as _______, permease as _______, and transacetylase as _______. The gene for the lac repressor (_______) is linked to the rest of the lac operon

A

lacZ, lacY, lacA, lacl

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22
Q

The lac operon is _______ regulated by a _______ protein.

A

negatively, repressor

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23
Q

The lac repressor binds to the _______ to block transcription. In the presence of lactose, an inducer molecule (_______) binds to the repressor protein. The repressor can no longer bind to the _______ and transcription proceeds

A

operator, allolactose, operator

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24
Q

_______ _______ is a mechanism for the preferential use of glucose in the presence of other sugars.

A

Glucose repression

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25
Q

_______ _______ _______ (CAP) is an allosteric protein with cAMP as effector

A

Catabolic activator protein

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26
Q

The level of _______ in cells is reduced in the presence of glucose so that no stimulation of transcription from _______-responsive operons takes place.

A

cAMP, CAP

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27
Q

_______ _______ - The presence of glucose inhibits the transport of lactose into the cell, EVEN IF there is lactose present

A

Inducer exclusion

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28
Q

The _______ _______ encodes genes for the biosynthesis of tryptophan

A

trp operon

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29
Q

The trp operon is not expressed when the cell contains sufficient amounts of _______

A

tryptophan

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30
Q

The trp _______ is a helix-turn-helix protein that binds to the operator site adjacent to the trp _______

A

repressor, promoter

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31
Q

The trp operon is negatively regulated by the trp _______ protein. This protein binds to the _______ to block transcription. This binding process requires a _______ which is tryptophan.

A

repressor, operator, corepressor

32
Q

When tryptophan levels fall, the repressor can’t bind to the operator, so the operon is _______ (versus being induced).

A

derepressed

33
Q

Tryptophan binding increases the _______ between the two recognition helices, allowing the repressor to fit into two adjacent portions of the _______ _______ in DNA

A

distance, major groove

34
Q

In Eukaryotic regulation, the control of _______ is more complex. The major differences from prokaryotes is that Eukaryotes have DNA organized into _______ which complicates the protein-DNA interaction. Also, Eukaryotic transcription occurs in the _______ while translation occurs in the _______.

A

transcription, chromatin, nucleus, cytoplasm

35
Q

_______ transcription factors are named TF + roman numeral + letter. The roman numeral indicates which _______ _______ the TF interacts with.

A

General, RNA Polymerase

36
Q

General TF’s are necessary for the assembly of a transcription _______ and the recruitment of RNA Pol II to a _______

A

apparatus, promoter

37
Q

TFIID recognizes _______ _______ sequences

A

TATA box

37
Q

The initiation complex formed by _______ _______ _______ can initiate synthesis at a _______ level

A

General transcription factors, basal

38
Q

_______ _______ _______ act in a tissue- or time- dependent manner to stimulate higher levels of transcription than the basal level

A

Specific transcription factors

39
Q

Each specific TF consists of a _______-_______ domain and a separate _______ domain that interacts with the transcription apparatus. These domains are _______ in the protein

A

DNA-binding, activating, independent

40
Q

_______ form the binding sites for general TFs.

A

Promoters

41
Q

General TFs mediate the binding of RNA polymerase II to the _______

A

promoter

42
Q

_______ are the binding site of the specific TFs

A

Enhancers

43
Q

Specific TF’s act over large distances by bending DNA to form a loop to position the _______ closer to the _______

A

Enhancer, promoter

44
Q

Coactivators and mediators are required for the function of _______ _______

A

transcription factors

45
Q

The number of _______ is small compared to the number of TFs because one can be used with multiple TFs

A

coactivators

46
Q

The _______ is essential to some but not all TFs.

A

mediator

47
Q

Virtually all genes transcribed by _______ _______ _______ need the same suite of general TFs to assemble an _______ _______

A

initiation complex

48
Q

The ultimate level of transcription depends on the _______ _______ _______ that together make up the _______ _______

A

specific transcription factors, transcription complex

49
Q

In the Eukaryotic _______ structure, DNA is wound around histone proteins to form nucleosomes.

A

chromatin

50
Q

DNA is wound around _______ proteins to form _______ in the Eukaryotic chromatin structure

A

histone, nucleosomes

51
Q

_______ and _______ complicate the process of transcription by restricting the access of the transcription machinery to the DNA

A

Nucleosomes, histones

52
Q

Alterations in _______ structure are though to be the basis for epigenetics.

A

chromatin

53
Q

_______ alterations must persist in the absence of the initiating stimulus, and must be inherited through _______ _______.

A

Epigenetic, cell division

54
Q

_______ _______: High levels of it is correlated with inactive genes, and allele-specific gene expression in genomic imprinting is at least partially due to it.

A

DNA methylation

55
Q

Mammalian females inactivate one _______ _______ as a form of dosage compensation.

A

X chromosome

56
Q

There are four possible _______ that can be modified

A

histones

57
Q

_______, _______, and _______ are all possible histone modifications

A

Acetylation, methylation, phosphorylation

58
Q

In general, the histone modification _______ is correlated with active sites of transcription.

A

acetylation

59
Q

Some transcription coactivators have been shown to be _______ _______ (HATs). Transcription is increased by removing higher order _______ structure that would prevent transcription

A

Histone acetylases, chromatin

60
Q

Gene expressions can be controlled after transcription with: _______ RNA’s (miRNA and siRNA), _______ splicing, RNA _______, or _______ degredation

A

Small, alternative, editing, mRNA

61
Q

_______-_______ mutant alters developmental timing in C. elegans

A

lin-4

62
Q

lin-4 does not encode a protein product, instead it encodes two _______ _______ molecules

A

small RNA

63
Q

lin-4 RNA acts as a transcriptional _______ of an mRNA

A

repressor

64
Q

miRNA production begins with RNA pol II producing a transcript called the _______-_______

A

pri-miRNA

65
Q

miRNA folds back on itself to form a _______-and-_______ structure which is cleaved by _______ to form pre-miRNA

A

stem, loop, Drosha

66
Q

pre-miRNA is exported from the nucleus and cleaved by _______ to produce a short double stranded RNA containing the miRNA

A

Dicer

67
Q

miRNA is loaded into a protein complex called an _______ _______ _______ _______ (RISC)

A

RNA induced silencing complex

68
Q

RISC includes the RNA-binding protein _______, which interacts with the miRNA

A

Ago

69
Q

RISC is targeted to repress the expression of genes based on the sequence complementary to the _______. This complementary region is usually in the ___ untranslated region of genes

A

miRNA, 3’

70
Q

_______ _______ refers to small RNA gene silencing, and involves the production of _______

A

RNA interference, siRNAs

71
Q

Production of siRNA is similar to miRNAs, but siRNAs arise from a _______ double-stranded RNA. _______ cuts yield of multiple siRNAs which are loaded into _______. The target _______ is then cleaved by the siRNA

A

long, Dicer, RISC, mRNA

72
Q

_______ represses genes different from its origin

A

miRNA

73
Q

_______ tends to repress genes they were derived from

A

siRNA

74
Q

The editing of mature _______ transcripts can produce altered versions that are not truly encoded in the genome

A

mRNA

75
Q

In mammals, RNA editing involves the chemical modification of a base to change its _______-_______ properties

A

base-pairing

BIO 214 (8 decks)

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