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Applied Genetics > Regulatory Regions > Flashcards

Regulatory Regions Flashcards

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1
Q

what is the TSS

A

transcription start site

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2
Q

what is cis acting

A

function that occurs on same chromosome

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3
Q

what is trans acting

A

function that occurs on opposite chromosome

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4
Q

what are enhancers

A

short region (50-1500bp) of DNA that can bind activator proteins to trigger transcription of a gene

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5
Q

what are TADs

A

Topological Association Domains a way to understand organisation of a genome

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6
Q

what are promoters

A

regulatory regions of DNA upstream of a gene, which provide a control point for regulated gene transcription

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7
Q

what is in the coding region

A
  • 3’ end has the Poly A

- 5’ end has the cap structure

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8
Q

structure of prokaryotes replicated DNA strand -polycistronic mRNA

A

promoter
5’ end non-coding region
coding region for multiple proteins - cistrons
terminator

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9
Q

structure of eukaryotes replicated DNA strand - mRNA

A 
promoter
transcription start
5'cap
5' non-coding
coding region for one protein (exons)
introns
3' non-coding
poly A tail
transcription end point
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10
Q

what is the consensus sequence

A

segment of DNA that is conserved where different proteins bind to it

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11
Q

what make up the promoter elements

A

core promoter and proximal promoter

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12
Q

what is the core promoter

A

minimal portion of the promoter required to properly initiate transcription. Located around position -34

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13
Q

what is the proximal promoter

A

proximal sequence upstream of the gene that contains primary regulatory elements. Located around position -250

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14
Q

what does the prokaryote promoter consist of

A

TTGACA -35 element
TATAAT -10 element prinbow box
TSS (transcription start site)

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15
Q

what do most eukaryotic core promoters consist of

A
  1. a TATA (TATAA) box, usually within 50 bp from Transcription State Site, that binds to the TATA protein to begin transcription
  2. a CAAT box (CCAATC), general transcription factors bind to it and it is frequently absent from ubiquitous genes. Located in the proximal promoter
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16
Q

what does RNA polymerase II bind to

A

transcription factors

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17
Q

what transcription factor binds to TATAbox

A

TF II D -complex of 15 proteins that binds to TATA box

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18
Q

what transcription factor binds to another transcription factor

A

TF II B binds immediately upstream of TFIID

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19
Q

when can RNA polymerase interact with DNA

A

when TFIID on TATA and TFIIB on TFIID

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20
Q

how many proteins is RNA polymerase II made of

A

12

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21
Q

where is the proximal promoter

A

outside region where RNA polymerase binds

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22
Q

how is the proximal promoter formed

A

> CAAT box, found in many animal and some plant genes
Sp1 box and GC box in animals and AGGA box in plants
Bind transcription factors so DNA loops around to bring these into contact with the RNA polymerase

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23
Q

what makes up the minimal promoter

Study These Flashcards
A

Core promoter and proximal promoter

24
Q

what is the minimal promoter for

Study These Flashcards
A

necessary for expression

25
what makes expression levels low
without presence of extra control sequences located in distal promoter
26
where is the distal promoter
very ill defined area which can range from beyond 3’ end of the gene, through coding region of the gene, through core promoter, through proximal promoter, right up to and even into next gene
27
how long are enhancers and what do they do
Enhancers are short (50-1500 bp) regions of DNA that can bind to proteins to activate transcription or increase expression of gene
28
characteristics of enhancers examples
generally cis-acting can be upstream or downstream from the start site, even in introns orientation independent sometimes not located on same chromosome as gene they’re regulating
29
why are enhancers important examples
evolution of species role development, differentiation and growth of cells and tissues development robustness: survival of fruit flies when environmental disturbances take place
30
what are promoter silencers and what do they do
Silencers are antagonists of enhancers that, when bound to its proper transcription factors – repressors
31
how do silencers and enhancers differ
Silencers and enhancers may be in close proximity to each other or may even be the same region only differentiated by the transcription factor region binds to
32
how do silencers work
when repressor protein binds to silencer region of DNA, RNA polymerase is prevented from binding to promoter region
33
characteristics of promoter silencers
1. generally cis-acting 2. located between -20 to -2000bp upstream from gene 3. most commonly found upstream from start site; some maybe located in introns or exons of gene itself. Also present in 3’ UTR 4. there are two types
34
what are the two types of promoter silencers
classical silencer element | non-classical regulatory element
35
what is classical silencer element
gene is actively repressed by silencer element by interfering with general transcription factor GTF
36
what is the non-classical regulatory element
NRE passively repress the gene by inhibiting other elements upstream of the gene. Some are orientation dependent
37
what are promoter insulators
genetic boundary elements that block the interaction between enhancers and promoters
38
what do promoter insulators do
- determine set of genes and enhancer can influence - act by forming loops - prevent spread of heterochromatin from silenced gene to an actively transcribed gene
39
when are promoter insulators made
formed when two adjacent genes in chromosome have different patterns of transcription
40
where are the promoter insulators
- occurs via 3D structure of DNA | - present at boundary of topological association domains (TADs) which divide chromosome in ‘chromosome neighbourhoods’
41
what can lead to transposon duplication
Transposition often results in duplication of transposon
42
how many types of transposons are there
2
43
what are the types of transposons
``` class I or retrotransposons class II (DNA transposons) ```
44
what is the function of class I or retrotransposons
copy and paste; copied in 2 stages DNA to RNA; RNA is reversed transcribed to RNA (i.e. retroviruses, as HIV) - transposons with long terminal repeats - line I (transcribed by RNA pol II) - SINEs (transcribed by RNA pol III)
45
what is the function of class II (DNA transposons)
cut and paste; does not involve RNA intermediate. Transpositions catalysed by several transposase enzymes
46
what are transposase enzymes | what can they cause
mutagens that can damage genome and produce diseases like haemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy
47
what does epigenetics study
variations that are caused by external or environmental factors that turn genes on or off affecting how the cells read this genetic information changes that can be inherited or not changes that epigenetics study in relation to gene expression or cellular phenotype are not based in changes in sequences of DNA
48
what are covalent modifications
DNA methylation and hydroxymethylation; protein acetylation, methylation, phosphorylation, ubiquitination and sumoylation
49
what are RNA transcripts
product that (directly or indirectly) maintains the activity of that gene
50
what are microRNAs
Non-coding RNAs of 17-25 nucleotides long
51
what is mRNA methylation
mRNA plays a critical role in human energy homeostasis, sRNAs
52
what are sRNAs
(50-250 nucleotides) virulence genes in pathogens
53
what are prions
infectious forms of proteins
54
what is structural inheritance
seems existing structures act as templates for new structures
55
what is nucleosome positioning
isn’t random | determine DNA accessibility to regulatory proteins determines differences in gene expression and cell differentiation

Applied Genetics (20 decks)

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