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Genetics - Lecture > 3.1. Gene Regulation > Flashcards

3.1. Gene Regulation Flashcards

1
Q

describe the regulation of gene expression in eukaryotes

A

(1) tightly controlled
(2) expression of the required levels of gene products
🔸at specific times
🔸in specific cell types
🔸in response to complex changes in the environment

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2
Q

eukaryotic gene expression is influenced by ____.

A

chromatin modifications

the presence of compact chromatin structures inhibits processes like DNA replication, repair, and transcription. hence, eukaryotic cells must modify their chromatin in order to regulate gene expression

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3
Q

(1) type of chromatin that can be transcribed
(2) type of chromatin that cannot be transcribed

A

(1) open chromatin
(2) closed chromatin

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4
Q

different mechanisms of chromatin modification

A

(1) histone modification
(2) modification of nucleosome composition
(3) chromatin remodeling complex
(4) DNA methylation

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5
Q

chromatin modification : covalent addition of functional groups to the n-terminal tails of histone proteins

A

histone modification

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6
Q

types of histone modification and their respective effects

A

(1) acetylation : gene activation
(2) methylation : increased or decreased gene repression
(3) phosphorylation : generally associated with gene activation

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7
Q

chromatin modification : modification of nucleosome composition

A

changing the composition of the nucleosome; chromatin composition switches between open and closed
example: variant histone (H2A.Z)
🔸affects nucleosome mobility and positioning
🔸may either activate or repress a gene promoter

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8
Q

chromatin modification : large multi-subunit complex that reposition nucleosomes, making regions of the chromosome accessible to transcription regulatory proteins; atp-mediated

A

chromatin remodeling complex

this complex use the energy of ATP hydrolysis to move

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9
Q

different mechanisms by which chromatin remodelers use ATP to alter nucleosome structure

A

(1) alteration of DNA-histone contacts
🔸chromatin remodelers convert ATP to ADP, which provides the energy needed to slide the nucleosome along the DNA; this sliding action exposes a segment of DNA, making it accessible for processes like transcription, replication, or repair
(2) alteration of the DNA path
🔸chromatin remodeler pulls DNA off the nucleosome using energy from ATP hdyrolysis; this alters the path of the DNA, exposing regions of the DNA sequence
(3) remodeling of nucleosome core particle
🔸energy from ATP hydrolysis is used by the chromatin remodeler to restructure the nucleosome core particle, leading to the formation of nucleosome dimers which exposes a segment of DNA

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10
Q

chromatin modification : enzyme-mediated addition or removal of methyl groups to or from the DNA bases

A

DNA methylation

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11
Q

in which organisms is DNA methylation observed?

A

(1) humans
(2) mice
(3) many plants
(4) inactivated x chromosome in female mammalian cells

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12
Q

where does DNA methylation most often occur?

A

position 5 of cytosine (5-methylcytosine) within CG doublets in DNA, usually on both strands
5′- mCpG- 3′
3′- GpCm - 5′

this position causes the methyl group to protrude into the major groove of the DNA helix

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13
Q

what are CpG islands?

A

CpG-rich regions often located in or near promoter regions

CpG sequence are NOT randomly distributed throughout the genome

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14
Q

how does DNA methylation affects gene expression?

A

DNA methylation represses gene expression
🔸when CpG island is methylated, gene expression is turned off, which means the gene adjacent to the methylated CpG island is not transcribed into RNA, and consequently, the protein encoded by this gene is not produced

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15
Q

DNA methylation mechanisms

A

(1) inhibition of binding of transcription factors to DNA : no transcription factors, no gene expression
(2) recruits repressive chromatin remodeling complexes : remember: chromatin r. modifies chrom. structure. these complexes then make the DNA less accessible to the transcription macinery
(3) recruits histone deacetylase (HDAC) to gene-regulatory regions : removal of acetyl groups from histone proteins leading to a more compact chromatin structure

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16
Q

generally, how are genes transcribed by RNAP II regulated?

A

regulatory factors bind to specific DNA sequences in the genes

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17
Q

types of RNAP II regulatory factors

A

(1) cis-acting DNA elements
(2) trans-acting factors

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18
Q

what are cis-acting DNA elements?

A

located on the same chromosome as the gene that they regulate

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19
Q

types of cis-acting DNA elements

A

(1) promoter and promoter elements
(2) enhancer elements
(3) silencer elements

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20
Q

a region of DNA that is recognized and bound by the basic transcriptional machinery and are required for transcription initiation

A

promoter

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21
Q

where are promoters located? why are promoters significant?

A

adjacent to the genes that they regulate (upstream); promoters are important as they:
(1) specify the site or sites (TSS) at which transcription begins
(2) specify the direction of transcription along the DNA

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22
Q

subcategories of eukaryotic promoters

A

(1) core promoters
(2) proximal promoter elements

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23
Q

minimum part of the promoter needed for accurate initiation of transcription by RNAP II

A

core promoter

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24
Q

length of core promoters

A

~ 80 nucleotides long

core promoters are sequences

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25
true or false : core promoters include the transcription start site (TSS).
true
26
types of core promoters with respect to TSS
(1) focused core promoters (2) dispersed core promoters
27
differentiate focused core promoters from dispersed core promoters. based on their (1) function, (2) occurrence in organisms, and (3) types of genes they are associated with
(1) function focused core promoters : specify transcription **initiation at a single specific start site** *whereas* dispersed core promoters : direct **initiation from a number of weak transcription start sites** located over a 50- to 100- nucleotide region (2) occurrence in organisms most genes of **lower eukaryotes** use focused core promoters *whereas* over **70% of vertebrates** employ dispersed promoters (3) types of genes they are associated with focused core promoters : usually associated with **genes whose transcription levels are highly regulated in terms of time or place** *whereas* dispersed core promoters are associated with **genes that are transcribed constitutively, known as housekeeping genes, whose expression is required in almost all cell types** ## Footnote a single TSS may facilitate precise regulation of some genes, whereas multiple start sites may allow for a steady level of transcription of genes that are requireed constitutively
28
true or false : it is not yet clear how dispersed core promoters specify multiple TSS.
true
29
describe the structure of focused core promoters
contains common core promoter elements : (1) TFIIB recognition element (2) initiator element (3) motif ten element (4) downstream promoter element
30
subcategory of eukaryotic promoters that are located up to 250 nucleotides upstream of the TSS, TATA box, and BRE of many genes
proximal promoter elements
31
proximal promoter elements contain binding sites for sequence-specific DNA-binding proteins. how are these proteins significant?
these DNA-binding proteins, known as transcription factors, **modulate the efficiency of transcription**
32
proximal promoter elements work in conjunction with core-promoter elements. how does this affect transcription?
the levels of basal transcription are increased
33
type of cis acting element that serve to regulate gene on the same chromosome; can be located on either side of a gene, nearby, or at some distance from the gene, or even within the gene
enhancer elements
34
true or false : while promoter sequences are essential for minimal or basal-level transcription, enhancers increase transcription rate and often confer time- and tissue-specific gene expression.
true
35
true or false : both promoters and enhancers can be found upstream of the genes they regulate
false ## Footnote position of enchancer is not critical; functions the same wherever
36
true or false : promoters are orientation specific. enhancers can be inverted relative to the gene it regulates
true ## Footnote enhancers can be inverted relative to the gene it regulates without a significant effect on its action
36
type of cis-acting element that acts as a negative regulator of transcription; may be located far upstream, downstream, or within the genes they regulate; often act in tissue- or temporal- specific ways to control gene expression
silencer
36
regulatory proteins that can fine-tune the levels and timing of transcription initiation; they can regulate a gene on any chromosome as appropriatefor (1) different cell types, (2) in response to environmental cues, and (3) developmental stages
trans-acting factors; also broadly called transcription factors
37
types of transcription factors
(1) general transcription factors (GTFs) (2) activators (3) repressors
38
type of transcription factor that is required for the basic process of transcription inititation
general transcription factors (GTFs) ## Footnote GTFs for RNAP II * TFIIA * TFIIB * TFIID * TFIIE * TFIIF * TFIIH * Mediator
39
type of transcription factor that increases the levels of transcription initiation
activators
40
type of transcription factor that reduces transcription levels
repressors
41
modification of eukaryotic nuclear RNA transcripts prior to translation
posttranscriptional regulation
42
general aspects of posttranscriptional regulation
mRNA processing -> transport to the cytoplasm -> mRNA stability
43
mRNA processing
(1) addition of 7-methylguanosine cap (5' end) (2) addition of poly-a tail (3' end) (3) splicing
44
process of splicing pre-mRNAs in alternative ways to generate different spliceforms
alternative splicing
45
alternative splicing enables a single gene to encode more than one variant of its protein product. what are these variants called?
isoforms
46
true or false : isoforms differ in the amino acids. despite this, they still possess similar functions.
false. isoforms have different functions due to variations in their amino acid sequences
47
true or false : isoforms are cell-specific.
true
48
types of alternative splicing
(1) cassette exons (2) alternative 5' or 3' splice site (3) intron retention (4) utually exclusive exons (5) alternative promoters (6) alternative polyadenylation
49
explain alternative splicing via casette exons
casette exons may be excluded from the mature mRNA by joining the 3' end of the upstream exon to the 5' end of the downstream exon; **casette exons are removed and ends are joined together** ## Footnote casette exons are segments of RNA that can be excluded or included during splicing
50
explain alternative splicing via alternative 5' or 3' splice site
mediated by the joining of exons at alternative 5' or 3' splice sites
51
explain alternative splicing via intron retention
non-coding portions of a gene may be retained in the final mRNA transcript
52
explain alternative splicing via mutually exclusive exons
only one of the two exons remains in mature mRNAs after splicing; inclusion of one exon leads to the exclusion of others in the same cluster
53
explain alternative splicing via alternative promoters
some genes have alternative promoters, so they have more than one site where transcription is initiated. this produces pre-mRNAs eith different 5' exons which can then be alternatively spliced to generate mRNA isoforms
54
explain alternative splicing via alternative polyadenylation
pre-mRNA can have multiple possible polyadenylation (polyA) sites, resulting in mRNA isoforms with different 3' ends
55
alternative splicing regulation is mediated by a class of proteins that bind to specific RNA sequences or RNA secondary structures and often exhibit tissue-specific expression. how are these proteins called?
RNA-binding proteins (RBPs)
56
mechanisms of RBPs
(1) **binding and hiding splice sites** to promote the use of alternative sites (2) **binding near alternative splice sites** to recruit the spliceosomes to such sites (3) **directly interacting** with the splicing machinery
57
what happens with aberrant mRNA, such as those with no poly-A tail or are improperly spliced?
(1) allow more time for processing (2) exoribonuclease degradation
58
true or false : the stability of mRNAs can vary greatly.
true. some may be very short-lived, lasting only a few minutes, while others can be quite stable, persisting for several days.
59
true or false : cells can regulate mRNA stability in response to various signals and needs.
true. for example, during stress conditions, certain mRNAs might be stabilized to ensure the production of stress-response proteins.
60
mechanisms of mRNA degradation
(1) exoribonuclease (2) deadenylation-dependent decay (3) deadenylation-independent decay (4) nonsense-mediated decay
61
enzymes that degrade RNA via the removal of terminal nucleotides
exoribonuclease
62
what features of mRNAs provide protection against exoribonuclease?
7-methylguanosine and poly-A tail ## Footnote removal of these components is required for mRNA decay
63
deadenylation-dependent decay is inititated by what enzyme?
deadenylase
64
how does deadenylase induce decay?
the enzyme deadenylase shortens the poly-a tail. if deadenylase shortens the tail to <30 nucleotides, mRNA will be degraded
65
how does deadenylation-independent decay occur?
(1) **decapping enzymes** remove the cap and **XRN1 exoribonuclease** digests the mRNA in the 5' to 3' direction (2) mRNAs may also be cleaved internally by **endoribonuclease**, and newly formed 5’ and 3’ ends are digested by **exoribonuclease**
66
how does nonsense-mediated decay work?
🔸once premature stop codons are identified, mRNAs possessing them are degraded 🔸in yeast and mammalian cells, decay is most often initiated by a **decapping enzyme or deadenylase**, followed by rapid **exoribonuclease digestion**
67
translational regulation
(1) direct regulation : ensures that specific mRNAs are translated at appropriate rates (2) protein quantity : modulates the amount of protein produced to meet cellular demands (3) highly regulated translation initiation (4) influenced by mRNA localization
68
effect of mRNA localization ## Footnote some mRNAs are localized to discrete regions of the cell where they are translated locally
cells can generate **asymmetric protein distributions** that enable different parts of the cell to have **different functions**
69
regulation of mRNA localization is mediated by ____.
cis-regulatory sequences on the mRNA and RNA-binding proteins e.g. actin mRNA (cell periphery) and neurons mRNA
70
mechanisms of posttranslational regulation
(1) covalent attachment to various molecules (2) phosphorylation (3) ubiquitin-mediated protein degradation
71
effects of covalent attachment of various molecules
(1) changes protein stability (2) changes subcellular localization (3) changes affinity for other molecules
72
most common type (65%) of posttranslational regulation which involves the addition of phosphate group to serine, tyrosine, or threonine amino acid side chains via **kinase**
phosphorylation
73
true or false : phosphorylation is irreversible
false. phosphorylation is reversible
74
effect of phosphorylation
induces conformational changes that alter substrate binding or DNA affinity
75
how does ubiquitin-mediated protein degradation work?
eukaryotic cell targets a protein for degradation via **ubiquitin**, a small protein found in all eukaryotes 🔸ubiquitin is covalently attached to a target protein 🔸long poly-ubiquitin chains are formed, which serves as "tags" that mark the protein for destruction 🔸**poly-ubiquinated proteins**, which are marked for destruction, are recognized by **proteasome**, a protein with protease activity 🔸proteasome destroys the target protein
76
ubiquitin is covalently attached to a target protein via a lysine side chain through a process called ___.
ubiquitination
77
mediators of transcriptional regulation in prokaryotes
(1) transcription factors : activators and repressors 🔸activator : turns transcription on; helps recruit sigma factors to a specific promoter region; effector is inducer 🔸repressor : turns transcription off; binds the operator region; effector is corepressor (2) effectors : inducer and corepressor; facilitate binding of transcription factors to the DNA
78
a regulatory mechanism that assesses population density; observed in *Aliivibrio fischeri and Pseudomonas aeruginosa*
quorum sensing system
79
true or false : there should be sufficient cell numbers of their own species before inititating quorum sensing
true
80
gene regulation in response to environmental conditions wherein environmental signals are detected by **cell surface sensing system**; e.g., two-component regulatory systems
signal transduction system
81
regulatory mechanisms that respond to environmental signals; regulate the transcription of many different genes comprising more than one regulon
global control system
82
type of regulation wherein RNA is employed to regulate gene expression; can occur at various stages, including transcription and translation
RNA-based regulation
83
an example of RNA-based regulation wherein the process of transcription is prematurely terminated; the rate of transcription is ultimately influenced by the rate of translation; e.g. tryptophan synthesis
attenuation
84
a short peptide containing two tryptophan residues near its terminus and functions as an attenuator
leader peptide

Genetics - Lecture (12 decks)

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