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Genetics > Exam 2 Control of Gene Expression > Flashcards

Exam 2 Control of Gene Expression Flashcards

1
Q

for proks, gene expression is often regulated through _

A

operons; group of genes that function together and are activated as a group

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2
Q

define structural genes

A

physically are structural (ex tubulin) or do perform a function (ex enzyme)

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3
Q

define regulatory genes

A

genes that encode products that interact with other sequences and affect the transcription and translation of the sequences (ex TFs)

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4
Q

define regulatory elements

A

dna seqs that are not transcribed but play a role in regulating other nucleotide sequences (regulate transcription of gene seqs at other locations in the genome)

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5
Q

define constitutive expression

A

genes active all the time; continuously expressed under normal cellular conditions (ex housekeeping genes, every cell type has these genes)

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6
Q

define positive control

A

stimulate gene expression

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7
Q

define negative control

A

inhibit gene expression

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8
Q

t/f: gene expression can be controlled at multiple levels

A

true

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9
Q

what is the initial level of gene control

A

chromatin condensation = genes are inaccessible to transcription machinery

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10
Q

encoded in the flanking seq around the dna are information that cause:

A

biochemical changes (histones) in order to favor transcription and TFs can identify the relaxed dna to initiate transcription (binding sites)

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11
Q

what are domains

A

dna-binding protein has domains; roughly 60-90 aas, responsible for binding to dna (very specific to dna seqs) and forms hydrogen bonds w/ dna. has many members so subtle variation in nucleotides for specificity

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12
Q

what is a motif:

A

dna-binding protein has a motif w/in binding domain; simple structure that fits into major groove of the dna (H+ bonds); physical interaction btwn structure of protein and structure of dna

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13
Q

dna-binding proteins can be grouped into several types based off of their _

A

structures, or motifs

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14
Q

operon structure

A

promoter + additional seqs that control transcription (operator) + structural genes

linear seq of genes w/ no intervening seq to stop transcription

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15
Q

what is a promoter

A

a region of dna that initiates transcription of a particular gene, located near the transcription start site of a gene, on the same strand and upstream of the start codon

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16
Q

typically, how long is a promoter

A

100-1000 base pairs long

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17
Q

define regulator gene

A

dna seq encoding products that affect the operon function but are not part of the operon

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18
Q

what helps produce the large phenotypic differences between humans and chimpanzees

A

changes in a relatively small number of regulatory seqs

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19
Q

euks differ from proks how?

A
  • each structural gene has its own promoter and is transcribed separately
  • dna must unwind from the histone proteins before transcription
  • transcription (nucleus) and translation (cytoplasm) are separated in time and space
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20
Q

DNase I hypersensitivity

A

sites that are unwound and separate from histone proteins are sensitive to DNase bc these sites are relaxed; DNase I hypersensitive sites: more open chromatin configuration site, upstream of the transcription start site

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21
Q

histone modification

A
  • addition of methyl groups to the histone protein tails (inhibitory)
  • addition of acetyl groups to histone proteins (relax)
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22
Q

what does histone acetylation accomplish

A

changes the charge and loosens histone interaction with DNA for transcription to occur

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23
Q

DNase sensitive regions have been shown to include many types of cis-regulatory elements including:

A

promoters, enhancers, insulators, silencers, and locus control regions (non-coding)

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24
Q

_ protects DNA from the nuclease

A

protein binding

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25
chromatin remodeling complexes accomplish:
reposition the nucleosomes, allowing TFs and RNA polymerase to bind to promoters and initiate transcription
26
_ changes histone properties
biochemical modification
27
the _ of histone proteins alters chromatin structure and permits some TFs to bind to dna
acetylation (acetyl groups to tails of histone proteins)
28
positively charged tails of nucleosomal histone proteins interact w/ the negatively charged phosphate groups of dna, so when acetylation of histones occurs, what happens?
alters the charge and therefore chromatin structure and permits some TFs to bind to DNA
29
define chromatin remodeling
chromatin remodeling complexes: bind directly to DNA sites and reposition nucleosomes
30
define dna methylation
dna methylation of CYTOSINE bases adjacent to guanine nucleotides (CpG)-CpG islands (usu associated w/ gene repression)
31
chromatin immunoprecipitation (ChIP) can be used to identify:
dna-binding sites of a specific protein and the locations of modified histone proteins - study the nature of modification and associated change in dna function - recognizes methyl-ed or acetyl-ed dna; can see which genes have been modified
32
what is selectively immunoprecipitated (ChIP) from the cell debris from use of an appropriate protein-specific antibody
cross-linked dna fragments associated with the protein(s) of interest
33
_ contain the information to modify gene expression
noncoding seqs
34
_ interacts with basal machinery to initiate transcription
TFs; transcriptional activators and coactivators stimulate and stabilize basal transcription apparatus at core promoter
35
define mediator
is a multiprotein complex that functions as a transcriptional coactivator in all euks. the main fcn of a mediator complex is to transmit signals from the TFs to the polymerase (position the polymerase)
36
regulation of galactose metabolism through
GAL4
37
transcriptional activator proteins bind to _ and stimulate _
bind to sites on DNA and stimulate transcription *most act by stimulating or stabilizing the assembly of the basal transcription apparatus)
38
what is important about a consensus seq
the consensus seq in a promoter (can be more than 1) illustrate that different seqs can be mixed and matched in different combinations; a different transcriptional activator protein binds to each consensus seq, and so each promoter responds to a unique combination of activator proteins
39
activation of GAL4 occurs via:
transcription is activated by GAL4 in response to galactose; GAL4 binds to the upstream activation seq site and controls the transcription of genes in galactose metabolism *when galactose is present, it binds to GAL3 and brings about a change in the conformation of GAL80 (inhibitor) so GAL4 can now interact w/ basal transcription apparatus to stimulate transcription*
40
transcriptional repressors bind to _
silencers (silencer region is a piece of dna that repressors bind to)
41
define enhancer
dna seq stimulating transcription a distance away from promoter (long way away from dna seq being stimulated)
42
define insulator
dna seq that blocks or insulates the effect of enhancers (do not need every gene activated on a dna seq)
43
a promoter is a positive control because:
it lies in front of the gene needed to be transcribed
44
an insulator blocks the action of an enhancer on a promoter when the insulator:
lies between the enhancer and the promoter
45
multiple response elements (MREs) are found in the _ region of the metallothionein gene
upstream
46
in response to heavy metals (physiological or xenobiotic)
these stimuli stimulate activator proteins that bind to several MREs and stimulate transcription; various proteins may bind to upstream response elements to stimulate transcription
47
environmental response elements are composed of _
consensus sequences (w/in their promoter seq) which are found across our genome to help cells deal with stress; help initiate transcription to turn of response element (ex heat shock element)
48
regulation of transcriptional stalling and elongation
heat shock proteins - transcription stalls near start codon when there is no environmental stress. stress causes polymerase release and rapid upregulation of transcription.
49
coordinated gene regulation
e.g. steroid response elements; euks have a set of genes that work together i.e. in various genes, their promoter contains response elements that can be activated together (can contain all the same response elements so can be coordinated)
50
response elements:
common regulatory elements upstream of the start sites of a collective group of genes in response to a common environmental stimulus
51
alternative splicing:
depending on conditions of the cell, can leave in or cut out a codon (different combinations) that will change function of the protein but still retain the reading frame w/o ruining C-terminal domain (will not be out of frame)
52
alternative splicing in the T-antigen gene
in response to mammalian virus SV40, the production of small or large T-antigen occurs. exons that are always there, i.e. constitutive, will remain but depending on use of splice site, an exon will remain or be removed
53
gene function can be regulated by _
alternative splicing
54
alternative splicing occurs in every category of _ hallmarks
cancer
55
VEGF alternative splicing regulates _
angiogenesis in tumor cells
56
what is a miRNA
microRNA; a small non-coding RNA molecule (containing about 22 nucleotides) that functions in RNA silencing and post-transcriptional regulation of gene expression
57
RNA silencing leads to:
the degradation of mRNA or to the inhibition of translation or transcription
58
double-stranded RNA (steps in its degradation)
1. cleaved by the enzyme Dicer to produce small interfering RNAs (siRNAs) 2. the siRNAs combine with protein to form a RISC (RNA-induced silencing complex) and pair w/ complementary seqs on mRNA 3. the complex cleaves the mRNA 4. after cleavage, the RNA is degraded
59
some genes are regulated by processes that affect translation or by modification of proteins, proteins bind 5' UTR and affect availability of translation machinery which causes:
an increase in availability of initiation factors which allows ribosomes to bind to mRNA and carry out translation which increases protein synthesis which can lead to cell proliferation (ex T-cell proliferation in response to antigen/virus) *the expression of some euk genes is regulated by the availability of components rqd for translation*
60
comparison of gene control in bacteria and euks: presence of operons
proks: common euks: uncommon
61
comparison of gene control in bacteria and euks: neg and pos control
proks: present euks: present
62
comparison of gene control in bacteria and euks: initiation of transcription
proks: relatively simple euks: relatively complex
63
comparison of gene control in bacteria and euks: enhancers
proks: less common euks: more common
64
comparison of gene control in bacteria and euks: transcription and translation
proks: occur simultaneously euks: occur separately
65
comparison of gene control in bacteria and euks: regulation by small RNAs
proks: rare euks: common
66
comparison of gene control in bacteria and euks: levels of regulation
proks: primarily transcription euks: many levels
67
comparison of gene control in bacteria and euks: cascade of gene regulation
proks: present euks: present
68
comparison of gene control in bacteria and euks: dna-binding proteins
proks: important euks: important
69
comparison of gene control in bacteria and euks: role of chromatin structure
proks: absent euks: important
70
development: cis-regulatory elements (promoter seqs) containing _ sites are bound by _
containing DNA BINDING SITES are bound by TFs and MODULATE THE ASSEMBLY OF PRE-INITIATION COMPLEX at promoters through physical contacts driven by 3D ARRANGEMENT of chromatin thereby acting as a molecular platform btwn cellular signaling and gene activity
71
Q: most transcriptional activator proteins affect transcription by interacting with
the basal transcription apparatus
72
Q: how do aas in dna-binding proteins interact w/ dna
by forming hydrogen bonds with dna bases
73
Q: what is the difference btwn a structural gene and a regulator gene
structural genes encode proteins that function in the structure of the cell; regulator genes control transcription of other genes
74
Q: in RNA silencing, siRNAs and miRNAs usu bind to which part of the mRNA molecules that they control
3' UTR

Genetics (37 decks)

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