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Genetics - Lecture > 3.1. Gene Regulation > Flashcards

3.1. Gene Regulation Flashcards

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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
Q

true or false : core promoters include the transcription start site (TSS).

A

true

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26
Q

types of core promoters with respect to TSS

A

(1) focused core promoters
(2) dispersed core promoters

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27
Q

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

A

(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

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

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28
Q

true or false : it is not yet clear how dispersed core promoters specify multiple TSS.

A

true

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29
Q

describe the structure of focused core promoters

A

contains common core promoter elements

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30
Q

subcategory of eukaryotic promoters that are located up to 250 nucleotides upstream of the TSS, TATA box, and BRE of many genes

A

proximal promoter elements

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31
Q

proximal promoter elements contain binding sites for sequence-specific DNA-binding proteins. how are these proteins significant?

A

these DNA-binding proteins, known as transcription factors, modulate the efficiency of transcription

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32
Q

proximal promoter elements work in conjunction with core-promoter elements. how does this affect transcription?

A

the levels of basal transcription are increased

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33
Q

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

A

enhancer elements

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34
Q

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.

A

true

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35
Q

true or false : both promoters and enhancers can be found upstream of the genes they regulate

A

false

position of enchancer is not critical; functions the same wherever

36
Q

true or false : promoters are orientation specific. enhancers can be inverted relative to the gene it regulates

A

true

enhancers can be inverted relative to the gene it regulates without a significant effect on its action

36
Q

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

A

silencer

36
Q

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

A

trans-acting factors; also broadly called transcription factors

37
Q

types of transcription factors

A

(1) general transcription factors (GTFs)
(2) activators
(3) repressors

38
Q

type of transcription factor that is required for the basic process of transcription inititation

A

general transcription factors (GTFs)

GTFs for RNAP II
* TFIIA
* TFIIB
* TFIID
* TFIIE
* TFIIF
* TFIIH
* Mediator

39
Q

type of transcription factor that increases the levels of transcription initiation

A

activators

40
Q

type of transcription factor that reduces transcription levels

A

repressors

41
Q

modification of eukaryotic nuclear RNA transcripts prior to translation

A

posttranscriptional regulation

42
Q

general aspects of posttranscriptional regulation

A

mRNA processing -> transport to the cytoplasm -> mRNA stability

43
Q

mRNA processing

A

(1) addition of 7-methylguanosine cap (5’ end)
(2) addition of poly-a tail (3’ end)
(3) splicing

44
Q

process of splicing pre-mRNAs in alternative ways to generate different spliceforms

A

alternative splicing

45
Q

alternative splicing enables a single gene to encode more than one variant of its protein product. what are these variants called?

A

isoforms

46
Q

true or false : isoforms differ in the amino acids. despite this, they still possess similar functions.

A

false. isoforms have different functions due to variations in their aminoa cid sequences

47
Q

true or false : isoforms are cell-specific.

A

true

48
Q

types of alternative splicing

A

(1) cassette exons
(2) alternative 5’ or 3’ splice site
(3) intron retention
(4) utually exclusive exons
(5) alternative promoters
(6) alternative polyadenylation

49
Q

explain alternative splicing via casette exons

A

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

casette exons are segments of RNA that can be excluded or included during splicing

50
Q

explain alternative splicing via alternative 5’ or 3’ splice site

A

mediated by the joining of exons at alternative 5’ or 3’ splice sites

51
Q

explain alternative splicing via intron retention

A

non-coding portions of a gene may be retained in the final mRNA transcript

52
Q

explain alternative splicing via mutually exclusive exons

A

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
Q

explain alternative splicing via alternative promoters

A

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
Q

explain alternative splicing via alternative polyadenylation

A

pre-mRNA can have multiple possible polyadenylation (polyA) sites, resulting in mRNA isoforms with different 3’ ends

55
Q

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?

A

RNA-binding proteins (RBPs)

56
Q

mechanisms of RBPs

A

(1) binding and hiding splice sites to promote the use of alternative sites
(2) Binding near alternative splice sites to recruits the spliceosomes to such sites
(3) directly interacting with the splice machinery

57
Q

what happens with aberrant mRNA, such as those with no poly-A tail or are improperly spliced?

A

(1) allow more time for processing
(2) exoribonuclease degradation

58
Q

true or false : the stability of mRNAs can vary greatly.

A

true. some may be very short-lived, lasting only a few minutes, while others can be quite stable, persisting for several days.

59
Q

true or false : cells can regulate mRNA stability in response to various signals and needs.

A

true. for example, during stress conditions, certain mRNAs might be stabilized to ensure the production of stress-response proteins.

60
Q

mechanisms of mRNA degradation

A

(1) exoribonuclease
(2) deadenylation-dependent decay
(3) deadenylation-independent decay
(4) nonsense-mediated decay

61
Q

enzymes that degrade RNA via the removal of terminal nucleotides

A

exoribonuclease

62
Q

what features of mRNAs provide protection against exoribonuclease?

A

7-methylguanosine and poly-A tail

removal of these components is required for mRNA decay

63
Q

deadenylation-dependent decay is inititated by what enzyme?

A

deadenylase

64
Q

how does deadenylase induce decay?

A

the enzyme deadenylase shortens the poly-a tail. if deadenylase shortens the tail to <30 nucleotides, mRNA will be degraded

65
Q

how does deadenylation-independent decay occur?

A

(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
Q

how does nonsense-mediated decay work?

A

🔸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
Q

translational regulation

A

(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
Q

effect of mRNA localization

some mRNAs are localized to discrete regions of the cell
where they are translated locally

A

cells can generate asymmetric protein distributions that enable different parts of the cell to have different functions

69
Q

regulation of mRNA localization is mediated by ____.

A

cis-regulatory sequences on the mRNA and RNA-binding proteins
e.g. actin mRNA (cell periphery) and neurons mRNA

70
Q

mechanisms of posttranslational regulation

A

(1) covalent attachment to various molecules
(2) phosphorylation
(3) ubiquitin-mediated protein degradation

71
Q

effects of covalent attachment of various molecules

A

(1) changes protein stability
(2) changes subcellular localization
(3) changes affinity for other molecules

72
Q

most common type (65%) of posttranslation regulation which involves the addition of phosphate group to serine, tyrosine, or
threonine amino acid side chains via kinase

A

phosphorylation

73
Q

true or false : phosphorylation is irreversible

A

false. phosphorylation is reversible

74
Q

effect of phosphorylation

A

induces conformational changes that alter substrate binding or DNA affinity

75
Q

how does ubiquitin-mediated protein degradation work?

A

eukaryotid 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, whcih 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
Q

ubiquitin is covalently attached to a target protein via a lysine side chain through a process called ___.

A

ubiquitination

77
Q

mediators of transcriptional regulation in prokaryotes

A

(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
Q

a regulatory mechanism that assesses population density; observed in Aliivibrio fischeri and Pseudomonas aeruginosa

A

quorum sensing system

79
Q

true or false : there should be sufficient cell numbers of their own species before inititating quorum sensing

A

true

80
Q

gene regulation in response to environmental conditions wherein environmental signals are detected by cell surface sensing system; e.g., two-component regulatory systems

A

signal transduction system

81
Q

regulatory mechanisms that respond to environmental signals; regulate the transcription of many different genes comprising more than one regulon

A

global control system

82
Q

type of regulation wherein RNA is employed to regulate gene expression; can occur at various stages, including transcription and translation

A

RNA-based regulation

83
Q

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

A

attenuation

84
Q

a short peptide containing two tryptophan
residues near its terminus and functions as an attenuator

A

leader peptide

Genetics - Lecture (12 decks)

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