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Foundations of Biology II > Molecular Genetics: Gene Expression > Flashcards

Molecular Genetics: Gene Expression Flashcards

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1
Q

gene expression

A

when DNA information is converted into functional molecules

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2
Q

constitutive expression

A

always expressed

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3
Q

regulated expression

A

expressed sometimes or in some cells

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4
Q

regulation can occur at which levels

A

transcriptional, translational, post-translational

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5
Q

which level of regulation has the most immediate effect

A

post-translational, but energy costly

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6
Q

which level of regulation is the most energy efficient

A

transcriptional, but slow effect

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7
Q

transcriptional regulation

A

regulatory proteins bind to DNA and inhibit or trigger transcription

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8
Q

translational regulation

A

change in mRNA stability or change in translation speed

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9
Q

post-translational regulation

A

chemical modifications of protein

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10
Q

negative control

A

genes turned off by a repressor protein bound to the operator sequence (i.e. lac operon)

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11
Q

operon

A

set of co-regulated genes which share promoter and regulatory sequence and are co-transcribed onto single mRNA strand

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12
Q

how does glucose regulate the lac operon

A

inducer exclusion via allosteric regulation of the permease transport proteins

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13
Q

inducer

A

triggers gene expression (i.e. lactose in lac operon)

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14
Q

inducible negative regulation

A

lac operon - repressor blocks gene expression, inducer inhibits functioning of the repressor

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15
Q

repressible negative regulation

A

trp operon - trp (inducer) binds to repressor to allow the repressor to bind to the operator and block gene expression

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16
Q

positive control

A

gene expression turned on by activator protein binding to an initiator sequence (araoperon)

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17
Q

how is the ara operon positvely regulated

A

when arabinose is present binding of araC protein to initiator allows for transcription of araBAD

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18
Q

how is the ara operon negatively regulated

A

when arabinose is absent araC protein is in different conformation that binds to ara operon initiator and araC operator to block transcription of both

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19
Q

global gene regulation

A

coordinating expression of large sets of genes

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20
Q

examples of global gene regulation in prokaryotes

A

operons, sigmas, regulons

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21
Q

sigmas

A

different sigmas activated in reponse to envrionment - binds to different promoters to activate different groups of genes

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22
Q

regulons

A

sets of genes or operons that have separate promoters but are controlled by the same regulatory protein that bind to the same but separate regulatory sequences

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23
Q

SOS response under negative control

A

repressor lexA bound to the operators; in response to DNA damage the protein recA induces lexA to allow transcription of repair genes

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24
Q

two groupings of gene regulation in eukaryoets

A

regulation in the nucleus

regulation in the cytoplasm

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25
Q

methods for regulation in the nucleus of eukaryotes

A

transcriptional control, chromatin remodeling, RNA processing

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26
Q

methods for regulation in the cytoplasm of eukaryotes

A

mRNA stability, translational control, post-translational modifications

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27
Q

nucleosomes

A

“beads” of DNA wrapped around histones link by “string” of 80bp DNA linker

28
Q

core histones

A

2 H2A-H2B dimers and H3-H4 tetramer

29
Q

H1

A

linker histone that seals DNA to the core histones

30
Q

chromatin condensing

A

nucleosomes interact to form a 30nm fiber - loops around protein scaffold - condenses even further to form chromosomes during mitosis

31
Q

DNA methylation

A

DNA methyltransferase (DMT) adds methyl groups to DNA

32
Q

increased DNA methylation resuls in

A

condensed chromatin - reduced gene epression

33
Q

histone code hypothesis

A

gene expression is in part regulated by combination of chemical modification on histones

34
Q

histone-acetyl transferases (HATs)

A

add negatively charged acetyl groups to lysines in histone proteins

35
Q

how do HATs effect chromatin

A

acetyl groups weaken interaction between histone and DNA - chromatin decondensing

36
Q

chromatin remodeling complexes

A

use ATP to slide nucleosome along DNA or eject histones from chromatin to open up DNA for transcription

37
Q

transcription activators

A

bind to enhancers to recruit chromatin remodeling complexes to the correct place for transcription initiation

38
Q

epigenetic inheritence

A

patterns of inheritence that do not relate to the primary sequence of DNA

39
Q

maternal effects

A

mother’s environment can cause changes to chromatin in offspring during development that have lasting effects on offspring’s gene expression

40
Q

enhancers

A

regulatory sequence that activates transcription when bound by an activator

41
Q

silencers

A

regulatory sequence that inhibits transcription when bound by a repressor

42
Q

whats special about silencers and enhancers

A

unique to eukaryotes, can be far away from gene its regulating, can work if flipped backwards

43
Q

promoter-proximal elements

A

regulatory sequences that bind transcription factors and are located close to the promoter

44
Q

in eukaryotes co-regulated genes can share

A

enhancer, silencer, promoter-proximal element

45
Q

mediator

A

binds to basal and regulatory transcription factors

46
Q

splice variants

A

alternatively spliced primary transcripts

47
Q

isoforms

A

different proteins dependent on splice variants

48
Q

splicing factors

A

proteins that bind to RNA and can activate or repress splicing at specific sites

49
Q

mRNA stability

A

how long a mRNA stays intact - degradation occurs with removal of the tail or cap

50
Q

what maintains mRNA stability

A

regulatory proteins that can bind to mRNA

51
Q

RNA interference pathway

A

microRNAs or small interfering RNAs that bind to mRNA to target it for destruction or inhibits translation

52
Q

dicer

A

enzyme that cuts precursor miRNA or siRNA

53
Q

how do miRNAs and siRNAs interect with mRNA

A

guide strand binds to Argonaute protein which binds to target mRNA

54
Q

RISC

A

RNA induced silencing complex (mi/siRNA and Argonaute and other proteins)

55
Q

source of siRNA

A

endogenous (experimental) or exogenous (viral) double-stranded RNA

56
Q

specificity of siRNA

A

targets 1 RNA and binds specifically to target

57
Q

result of siRNA

A

mRNA degradation

58
Q

source of miRNA

A

small double stranded RNAs in the nucleus

59
Q

specificity of miRNA

A

targets multiple RNAs and has less specific binding

60
Q

result of miRNA

A

mRNA degradation or translation inhibition

61
Q

why is the RNAi pathway useful in biotech?

A

knock out mutants can be made without completely altering a gene

62
Q

what levels of gene regulation do eukaryotes have that prokaryotes don’t have

A

chromatin remodeling, RNA processing, mRNA stability

63
Q

what happens when RISC-miRNA binds to 3’ UTR

A

translation initiation blocked because formation of translation initiation factor complex is prevented

64
Q

what happens when RISC-miRNA binds to a different region of the mRNA

A

translation elongation is blocked

65
Q

methods of cell-wide reduction of translation

A

phosophorylation or ribosomes or EIFs (in translation initiation factor complex)

66
Q

ubiquitin-mediated proteolysis

A

proteins tagged with ubiquitin by ubiquitin ligases are recognized by the proteosome for destruction

Foundations of Biology II (17 decks)

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