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BIOL214 > chapter 16 > Flashcards

chapter 16 Flashcards

1
Q

transcription initiation

A

controlling gene expression is often accomplished by controlling this

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2
Q

regulatory proteins

A

bind to DNA, influence binding of RNA Pol II to promoter
- gain access to bases of DNA at major groove
- possess DNA-binding motifs
- block transcription by preventing RNA Pol II from binding, or stimulating transcription by facilitating RNA Pol II binding to promoter

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3
Q

prokaryotic organisms regulation

A

regulate gene expression in response to their environment

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4
Q

eukaryotic cells regulation

A

regulate gene expression to maintain homeostasis

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5
Q

eukaryotic - transcriptional regulation

A
  • chromatin remodels to make genes accessible for transcription
  • regulatory events at gene’s promoter and regulatory sequences

*determines which genes are transcribed.

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6
Q

eukaryotic - post-transcriptional regulation

A
  • removal of masking proteins
  • variations in rate of mRNA breakdown
  • RNA interference

*determines types and availability of mRNAs to ribosomes

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7
Q

eukaryotic - translational regulation

A
  • variations in rate of initiation of protein synthesis

*determines rate at which proteins are made

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8
Q

eukaryotic - posttranslational regulation

A
  • variations in rate of protein processing
  • removal of masking segments
  • variations in rate of protein breakdown

*determines availability of finished proteins

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9
Q

major groove of DNA

A
  • within the major groove, nucleotides’ hydrogen bond donors and acceptors are accessible
  • unique accessibility patterns for each base pair combination enable proteins to read sequence without unwinding DNA
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10
Q

DNA-binding motifs

A

regions of regulatory proteins which bind to DNA

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11
Q

helix-turn-helix motif

A

two alpha-helical segments linked by a non-helical segment

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12
Q

homeodomain

A

a special class of helix-turn-helix which is critical in eukaryotic development

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13
Q

zinc finger motif

A

several forms, use zinc atoms to coordinate DNA binding

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14
Q

leucine zipper motif

A

dimerization motif in which a region in one subunit interacts with similar region on other subunit to form zipper-like connection

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15
Q

prokaryotic regulation - transcription initiation

A

positive control: increases frequency of initiation -> activators enhance RNA Pol II binding to promoter

negative control: decreases frequency of initiation -> repressors bind to operators that prevent or decrease initiation frequency

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16
Q

operators

A

regulatory sites on DNA

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17
Q

effector molecules

A

can act on both repressors and activators

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18
Q

operons

A

genes involved in the same metabolic pathway

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19
Q

induction

A

(prokaryotes) enzymes for a certain path are produced in response to a substrate

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20
Q

repression

A

(prokaryotes) capable of making an enzyme but does not

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21
Q

lac operon

A
  • encodes proteins necessary for the use of lactose as an energy source

beta-galactosidase - lacZ
permease - lacY
transacetylase - lacA

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22
Q

lacI

A

lac repressor -> gene for lac repressor is linked to the rest of the lac operon

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23
Q

lac operon (negative regulation)

A

negatively regulated by a repressor protein
- lac repressor binds to operator to block transcription
- in the presence of lactose, allolactose (inducer) binds to repressor protein
- repressor can no longer bind to the operator so transcription proceeds

*in absence of lactose, lac operon expressed at a very low level

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24
Q

glucose repression

A

mechanism for the preferential use of glucose in the presence of other sugars (ex: lactose)
- glucose used first, then lactose

  • mechanism involves activator protein that stimulates transcription
  • CAP (catabolic activator protein) is an allosteric protein with cAMP as effector
  • level of cAMP in cells is reduced in the presence of glucose so that no stimulation of transcription from CAP-response operons takes place
25
Q

induce exclusion

A

presence of glucose inhibits transport of lactose into cell

26
Q

trp operon

A

encodes genes for biosynthesis of tryptophan

  • the operon is not expressed when the cell contains sufficient tryptophan
  • operon is expressed when tryptophan levels are low
27
Q

trp repressor

A

helix-turned-helix protein that binds to the operator site located adjacent to trp promoter

28
Q

negative regulation of trp operon by trp repressor protein

A
  • trp repressor binds to operator to block transcription
  • binding of repressor to operator requires a corepressor which is tryptophan (operator is repressed)
    when tryptophan levels fall, the repressor can’t bind to the operator (operator is depressed vs. being induced)
29
Q

tryptophan binding

A

*alters repressor conformation
- tryptophan binding increases distance between two recognition helices
- repressor can then fit snugly into two adjacent partitions of major groove in DNA

30
Q

eukaryotic transcription control

A

more complex than prokaryotes

31
Q

eukaryotic regulation vs prokaryotic regulation

A
  • eukaryotic DNA organized into chromatin which complicates protein-DNA interaction
  • transcription occurs in nucleus; translation in cytoplasm
  • amount of DNA involved in regulating eukaryotic genes is much larger
32
Q

transcription factor nomenclature

A

TF + roman numeral of which RNA polymerase (ex: TFIID - transcription factor RNA Pol II D)

33
Q

general transcription factors

A
  • necessary for assembly of a transcription apparatus and recruitment of RNA Pol II to a promoter
  • TFIID recognizes TATA box sequence
    after TFIID binds, TFIIE, TFIIF, TFIIA, TFIIB, and TFIIH bind; along with many transcription associated factors

*this complex can initiate synthesis at basal level

34
Q

specific transcription factors

A
  • act in a tissue specific or time-dependent manner to stimulate higher levels of transcription than the basal level
  • each factor consists of a DNA-binding domain and a separate activating domain that interacts with the transcription apparatus
35
Q

promoters

A
  • form binding sites for general transcription factors
  • mediate binding of RNA Pol II to the promoter
36
Q

enhancers

A
  • are the binding site of specific transcription factors
  • act over large distances by bending DNA to form loop to position enhancer closer to promoter
37
Q

coactivators

A
  • required for function of transcription factors
  • same coactivator can be used with multiple transcription factors (number of coactivators is less than transcription factors)
38
Q

mediators

A
  • required for function of transcription factors
  • essential to some but not all transcription factors
39
Q

transcription complex

A
  • nearly every eukaryotic gene represents a unique case
  • almost all genes that are transcribed by RNA Pol II need the same suite of general factors to assemble an initiation complex
  • ultimate level of transcription depends on specific transcription factors that make up the transcription complex
40
Q

eukaryotic chromatin structure

A
  • DNA wound around histone proteins to form nucleosomes
  • nucleosomes and histones complicate the process of transcription (restricts access of the transcription machinery to the DNA)
  • chromatin structure is selectively modulated to allow transcription
41
Q

epigenetic alterations

A
  • alterations in chromatin structure are thought to be the basis for heritable changes in phenotype (not due to changes in DNA sequence)
  • epigenetic alterations must persist in the absence of the initiating stimulus; must be inherited through cell division
42
Q

chromatin modifications

A

DNA methylation and X-chromosome inactivation

43
Q

DNA methylation

A

high levels of DNA methylation correlate with inactive genes
- allele specific gene expression seen in genomic imprinting is at least partially due to DNA methylation

44
Q

X-chromosome inactivation

A

-mammalian females inactivate one X chromosome as a form of dosage compensation
- long noncoding RNA called X-inactivation-specific transcript (Xist) coats the entire inactive X chromosome, leading to histone modification

45
Q

histone modifications

A

affects chromatin structure
- four possible histones can be modified
- acetylation, methylation, phosphorylation are all possible modifications

46
Q

acetylation

A

generally correlated with active sites of transcription

47
Q

histone acetylases (HATs)

A
  • some transcription coactivators have been shown to be HATs
  • transcription is increased by removing higher order chromatin structure that would prevent transcription
48
Q

histone deacetylases (HDACs)

A

remove acetyl groups from histones

49
Q

posttranscriptional regulation

A

control of gene expression usually involves the control of transcription initiation

50
Q

post transcriptional gene expression control mechanisms

A

small RNAs (miRNAs and siRNAS, alternative splicing, RNA editing, mRNA degradation

51
Q

small RNAs

A
  • lin-4 mutant alters developmental timing in C. elegans
  • lin-4 doesn’t encode a protein product; instead it encodes two small RNA molecules
  • lin-4 RNA acts as a transcriptional repressor of an mRNA
  • first discovered miRNA; many found subsequently (currently 1881 known human miRNA sequences)
52
Q

miRNA

A

micro-RNA
- production begins with RNA Pol II producing a transcript called pri-miRNA
- miRNA folds back on itself to form a stem and loop structure which is cleaved by Drosha to form pre-miRNA
- pre-miRNA exported from the nucleus and cleaved by Dicer to produce a short double-stranded RNA containing the miRNA

53
Q

RNA induced silencing complex

A
  • miRNA loaded into a protein complex called an RNA induced silencing complex (RISC)
  • RISC includes the RNA-binding protein Ago which interacts with the miRNA
  • RISC is targeted to repress the expression of genes based on sequence complementary to the miRNA (complementary region usually in 3’ untranslated region of genes)
54
Q

siRNA

A
  • RNA interference refers to small RNA gene silencing, involves the production of small interfering RNAs (siRNAs)
  • production similar to miRNAs but siRNAs arise from long double-stranded RNA
  • dicer cuts yield multiple siRNAs which are loaded into RISC
  • target mRNA is cleaved by siRNA containing RISC
55
Q

other roles of small RNA

A
  • protecting the genome (evolutionary origin of small RNAs show pathway for this)
  • RNA silencing pathways have been implicated in the formation of heterochromatin in different organisms
56
Q

difference between miRNA and siRNA

A
  • miRNA repress genes different from their origin
  • endogenous siRNA repress genes they were derived from
57
Q

alternative splicing

A

tissue specific
ex: same gene makes calcitonin in the thyroid and calcitonin-gene related peptide (CGRP) in the hypothalamus

58
Q

RNA editing

A
  • editing of mature mRNA transcripts can produce an altered mRNA that is not truly encoded in the genome
  • in mammals, RNA editing involves chemical modification of a base to change its base pairing properties

ex: the mRNA for the serotonin receptor is edited at multiple sites to produce 12 different isoforms of the protein

BIOL214 (4 decks)

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