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Genetics 380 > Gene Regulation in Eukaryotes > Flashcards

Gene Regulation in Eukaryotes Flashcards

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Biology 101 flashcards
1
Q

key to being complex organism

A

gene regulation not more genes

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2
Q

constitutive (housekeeping) genes

A

always on at all time in all cells (ex: actin and other genes that make components of the cytoskeleton, genes that make enzymes that carry out glycolysis)

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3
Q

inducible/repressible genes

A

level of activity changes as your needs change (ex: metallothionein and genes whose proteins clear metals can be induced by the presence of metal in the body)

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4
Q

tissue dependent gene regulation

A

responsible for differentiation of different tissue types; subset of genes that get turned on determine what proteins cell has which determines properties that cell has; tissue specific epigenetic difference in genes

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5
Q

cell division

A

cells become more specialized w every cell division

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6
Q

globin genes

A

time dependent gene regulation; gamma-Hb has higher affinity of O2 than beta-Hb which allows fetus’ Hb to take O2 out of the mother’s blood

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7
Q

biochemical individuality

A

differences in gene activity levels; gene regulation is variable btwn individuals so level of activity in most proteins variable btwn inds

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8
Q

epigenetic factors

A

regulation of gene express that does not involve changing the sequence of bases in the gene; factors that influence chromatin configuration

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9
Q

DNA packaging

A

chromatin config. changes to make promoter region more/less accessible to transcription factors

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10
Q

facultative heterochromatin

A

some heterochr regions packed as heterochr in one cell but euchr in another cell; some exist mostly as heterochr but can decondense temporarily and express genes in region in response to certain molecular signals

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11
Q

transcription initiation

A

interactions btwn regulatory sequences and transcriptional activators/inhibitors

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12
Q

RNA processing

A

alt cleavage and splicing of pre-RNAs

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13
Q

RNA stability

A

poly-A-tail and interferring RNAs regulate RNA longevity

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14
Q

translation initiation

A

5’ and 3’ UTRs and interfering RNAs regulate rate of translation

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15
Q

cis acting transcription regulation

A

lie on the same chr as the gene (ex: promoters, enhancers, insulators and other seqs that lie in the regulatory regions)

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16
Q

trans acting transcription regulation

A

produced elsewhere and bind the regulatory sequences (ex: activators, repressors that bind to promoter region or insulator binding proteins)

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17
Q

transcriptional activators/repressors

A

bind to reg promoter or enhance and can increase rate of transcription or keep the gene silenced

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18
Q

transcription factor protein complex and RNA polymerase

A

bind to core promoter and provide ability to transcribe but at minimal rate

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19
Q

step one in signal transduction

A

hormone binds to extracellular domain of receptor protein (surface of cell)

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20
Q

step two in signal transduction

A

receptor protein has intracellular domain that initiates biochemical cascade often involving phosphorylation of proteins inside cell

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21
Q

step three in signal transduction

A

biochemical cascade alters transcription factor and allow it to enter nucleus and activate/inhibit its target genes

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22
Q

response element

A

promoter seq. that is found in promoter regions of several genes whose proteins must work together; enable eukaryotes to regulate multiple genes simultaneously and coordinately regulated; one event (heat, stress) can activate/inhibit # of genes whose proteins help cell cope w the event

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23
Q

insulators

A

prevent gene activation by transcription factors

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24
Q

chromatin configuration

A

regulates gene activity: heterochromatin, euchromatin, supercondensation of heterochromatin; chromatin must be rearranged to allow transcription factor proteins and RNA polymerase to access the gene’s promoters (even in euchr)

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25
Q

regulatory sequences

A

must be accessible to transcription factors for transcription to occur

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26
Q

DNAse I

A

enzyme that cuts DNA next to each pyrimidine nucleotide (C and T) cuts DNA down to approx. 1-8 bp fragments; more relaxed chromatin is more sensitive to DNAse; more transcriptionally active regions are more sensitive to DNAse I

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27
Q

chromosome puffs

A

form in regions in which several genes are active for some species (ex: drosophila)

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28
Q

common chemical modifications

A

methylation of histones (often the lysines) acetylation of histone proteins (often at positively charged lysines) and methylation of DNA (often the Cs in CG island in the promoter region)

29
Q

methylation of histones

A

regulates transcription; can enable activation or repression of gene activity depending on specific amino acid that get methylated

30
Q

H3K4me3 methylation

A

3 methyl groups added to lysine number 4 in histone 3 aka H3K4me3 (K = lysine) enhance transcription; some proteins that bind to H3K4me3 decondense the local chromatin

31
Q

acetylation of histone proteins

A

makes DNA accessible to transcription factors

32
Q

chromatin remodeling complexes

A

control gene activity; complexes of transcription factors and other proteins that move nucleosomes around exposing promoter sites so transcription factors can bind them; some slide nucleosome down DNA exposing promoter region; some change conformation of DNA and/or nucleosome exposing promoter

33
Q

DNA methylation

A

inhibits transcription of genes in that region; methylation of cytosines in promoter regions of genes = prevents transcription factors from binding transcription doesn’t occur; 2-7% of all cytosines methylated in eukaryotes (not in drosophila or yeast)

34
Q

increased trinucleotide repeat

A

increases methylation and leads to fragile X syndrome; FMR1 gene has trinucleotide repeat (CGG) in promoter which can expand during meiosis; too many leads to increased methylation and deacetylation of histone protein inhibition of transcription of FMR1 and fragile X mental retardation syndrome

35
Q

X-inactivation

A

silences most of the genes on one X chromosome in humans; deleterious to development to have 2 active copies of every genes on X chromosome

36
Q

XIST RNA

A

X that gets inactivated produces this specific RNA called X-inactivation specific transcript XIST; coats chromosome super condenses and fosters methylation of promoter region

37
Q

TSIX RNA

A

produces by other X to protect itself; complementary to XIST RNA the two bind preventing XIST RNA from inactivating second X

38
Q

Barr body

A

super condensed inactivated X chromosome

39
Q

imprinted gene

A

regulated by different methylation of the promoter regions; methylation of Cs followed by Gs in CG islands represses transcription

40
Q

gametogenesis

A

during spermatogenesis and oogenesis DNA is completely unmethylated then remethylated in appropriate pattern that comes from parent of your sex; problems could result in 2 or 0 working copies of imprinted genes

41
Q

methylated DNA binding proteins

A

have domain that binds methylated DNA and domain that has histone deacetylase activity; tighten chromatin in regions where promoter region Cs are methylated

42
Q

MECP2

A

X linked gene mutations have sex influenced side effects; Rett syndrome in females

43
Q

Rett syndrome

A

cause by MECP2 mutation; normal development for approx. 6 months then regression of cognitive capabilities and head ceases to grow resulting in microcephaly; extremely variable expressed syndrome featuring cognitive impairment and other CNS features in males

44
Q

identical twins

A

develop different traits and different patterns of DNA methylation and histone acetylation

45
Q

early life experience & epigenetic factors

A

level of methylation of DNA influence by amount of licking rat receives during infancy; effects seen on glucocorticoid receptor gene/protein and offsprings’ responses to stress and persist into adulthood

46
Q

epigenetic factors & diet

A

bees and royal jelly: RJ silences DNA methyltransferase 3 gene (Dnmt3) which changes methylation of/expression of # of genes causing female to develop as queen and able to reproduce

47
Q

heritable epigenetic factors

A

pregnant woman w metabolic abnormality (diabetes, high blood lipids) can change methylation pattern of her genes and some of child’s genes; set as if child’s body is expecting to experience same nutrition after birth as before: after born does not metabolize nutrients optimally

48
Q

stressed female rat

A

changes in all generations; changes in methylation of glucocorticoid gene in offsprings’ brains

49
Q

gender & epigenetic factors

A

obese mom rat consistently obese daughters; obese father 15% obese daughters

50
Q

paramutation

A

heritable changes in gene expression due to epigenetic effects (ex: corn spotting)

51
Q

Kit(t) allele

A

produces microRNA that degrades the Kit mRNA; lethal

52
Q

Kit gene

A

contributes to pigmentation; heterozygotes have white tails and feet

53
Q

specialized DNA methyltransferases

A

maintain epigenetic changes through DNA replication; some specifically recognize and methylate hemimethylated DNA which methylates newly synthesized DNA strand

54
Q

complex organisms & more complex gene structure

A

ability to produce multiple proteins from single gene; different isoforms

55
Q

different isoforms

A

same active domains but different regulatory domains which allows different tissues to turn the protein on and off at different times; also have have different activities and perform different functions

56
Q

alternative splicing

A

allows one gene to make several different isoforms of its proteins; can let one gene make different proteins in different cells

57
Q

sex determination in drosophila

A

regulated by alternative splicing of transformer (Tra) gene mRNA by the sex-lethal (Sxl) protein

58
Q

poly-A binding proteins

A

bind to poly-A tail to stabilize mRNA but one tail shrinks to approx 10-30 As poly A binding proteins can’t bind to poly A tail any more and mRNA degrades; mRNA must be stabilize if they’re gonna remain in cytoplasm long enough to be translated

59
Q

interfering RNAs (iRNAs)

A

microRNAs (miRNAs) and small interfering RNAs (siRNAs); formed when longer double stranded RNA precursor is cleaved in cytoplasm by enzyme Dicer both join w proteins to make up RISC (RNA induced silencing complex); have base sequence that is complementary to some portion of either mRNA’s sequence or gene’s sequence so iRNA can bind to either mRNA or gene itself

60
Q

siRNAs

A

exogenous double stranded RNAs that are taken up by cells or enter via vectors like viruses

61
Q

miRNAs

A

single stranded and endogenous - transcribed from sequences in cell’s genome - some are found w/i introns of genes; some of what was once nonfunctional “junk” DNA has turned out to include miRNA encoding sequences

62
Q

inhibition of translation

A

if iRNA can bind to some portion of 5’ end of mRNA this will prevent ribosome from reading mRNA

63
Q

cleavage of mRNA

A

RISC complex includes endonucleases that cleave double stranded RNAs; if iRNA binds portion of mRNA endonucleases will cleave mRNA

64
Q

RISC complex

A

includes endonucleases that can cleave mRNA

65
Q

Fire and Mello

A

able to completely abolish protein production w concentration of iRNA that delivered approx. 2 molecules of iRNA per cell

66
Q

iRNAs & methylation

A

cause gene to be methylated inhibiting transcription; other iRNAs attach to complementary sequences in DNA and attract methylating enzymes which methylate DNA or histones and inhibit transcription; some inhibit protein production by unknown mechanism

67
Q

lincRNA-p21

A

represses action of transcription factor p53 which regulates number of genes whose proteins regulate cycle and apoptosis

68
Q

p53

A

dysfunction is involved in human cancer; regulates number of genes whose proteins regulate cycle and apoptosis

69
Q

ubiquitin

A

tags proteins for degradation; brings proteins to proteasome to be degraded - proteins that attach ubiquitin to specific target proteins can be increased or decreased altering the lifespan of the protein

Genetics 380 (11 decks)

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