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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
induce exclusion
presence of glucose inhibits transport of lactose into cell
26
trp operon
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
trp repressor
helix-turned-helix protein that binds to the operator site located adjacent to trp promoter
28
negative regulation of trp operon by trp repressor protein
- 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
tryptophan binding
*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
eukaryotic transcription control
more complex than prokaryotes
31
eukaryotic regulation vs prokaryotic regulation
- 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
transcription factor nomenclature
TF + roman numeral of which RNA polymerase (ex: TFIID - transcription factor RNA Pol II D)
33
general transcription factors
- 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
specific transcription factors
- 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
promoters
- form binding sites for general transcription factors - mediate binding of RNA Pol II to the promoter
36
enhancers
- 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
coactivators
- required for function of transcription factors - same coactivator can be used with multiple transcription factors (number of coactivators is less than transcription factors)
38
mediators
- required for function of transcription factors - essential to some but not all transcription factors
39
transcription complex
- 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
eukaryotic chromatin structure
- 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
epigenetic alterations
- 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
chromatin modifications
DNA methylation and X-chromosome inactivation
43
DNA methylation
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
X-chromosome inactivation
-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
histone modifications
affects chromatin structure - four possible histones can be modified - acetylation, methylation, phosphorylation are all possible modifications
46
acetylation
generally correlated with active sites of transcription
47
histone acetylases (HATs)
- some transcription coactivators have been shown to be HATs - transcription is increased by removing higher order chromatin structure that would prevent transcription
48
histone deacetylases (HDACs)
remove acetyl groups from histones
49
posttranscriptional regulation
control of gene expression usually involves the control of transcription initiation
50
post transcriptional gene expression control mechanisms
small RNAs (miRNAs and siRNAS, alternative splicing, RNA editing, mRNA degradation
51
small RNAs
- 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
miRNA
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
RNA induced silencing complex
- 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
siRNA
- 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
other roles of small RNA
- 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
difference between miRNA and siRNA
- miRNA repress genes different from their origin - endogenous siRNA repress genes they were derived from
57
alternative splicing
tissue specific ex: same gene makes calcitonin in the thyroid and calcitonin-gene related peptide (CGRP) in the hypothalamus
58
RNA editing
- 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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