Gene expression Flashcards by Phoebe Mountain

What does expression of genes depend on?

Tissue, developmental stage and intra/extracellular signals

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What genes are always expressed at constant levels?

Housekeeping genes

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What are 2 types of inducible genes?

Switched on in specific cell types (dependent on TFs)

Switched on in response to environmental cues

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What does gene expression regulate (binding)?

Ability of RNA polymerase to bind promoter

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How is bacterial transcription initiated?

Binding of sigma factor to promoter, enable RNA polymerase to bind and form preinitiiation complex.

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What determines whether sigma factors binds to prokaryotic promoter

Complementary of promoter region

Type of sigma factor

Repressor/activator protein

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How is bacterial DNA organised?

Operons - set of genes (for similar function) under control of one promoter

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What is the benefit to having no operons in eukaryotic DNA?

Genes encoding proteins for different steps in a pathway have their own promoter so expression can be modulated separately

Protective, one mutation unlikely to damage entire process

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What do operons contain?

Regulatory DNA sequences that are binding sites for regulatory proteins to control how much the operon is transcribed

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What do regulatory proteins do in prokaryotic transcription?

Repressors bind to operators, reducing transcription

Activators bind to DNA binding site and increases transcription

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Does prokaryotic DNA contain introns and exons?

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How can expression be altered based on modifications to chromatin, what part of chromatin is affected?

Chemical modifications to N terminal histone tails in nucleosomes by activators/repressors to change accessibility of TFs to DNA

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What happens in DNA methylation, what’s the result?

Methyltransferase converts cytosine to 5 cytosine

Methyl group disrupts binding of protiens needed for transcription

Chromatin becomes more compact and less accessible

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How are TSG often silenced?

Hypermethylation

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What is the difference between constituitively heterchromatic and facultative heterochromatic?

Constitutive: permanent

Faculative: can be converted to euchromatic

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Which have active genes heterochromatin or euchromatin?

Euchromatin

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Describe structure of chromatin in heterochromatin

Chromatin more condensed due to methylation

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What does methylation of chromatin also facilitate?

Binding of additional proteins

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What is constitutively heterochromatic?

Centromeres and telomeres (contain many tandem repeats)

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Example of facultative heterochromatin, how is it altered?

Inactive X chromosome inactivated to become heterochromatic state (barr body) by recruiting enzymes to modifty histones

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What is acetylated in gene expression?

Lysine residues of histone tails

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How does acetylation affect gene expression? (mechanism)

Neutralise + charge of histone tail so -ve charged DNA less tightly wrapped around histone /nucleosome and more accessible

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What does acetylation recruit?

Chromatin remodelling complexes - shift nucleosomes and induce chromatin conformational change

TATA box binding protein associated factors: affecting rate of transcription

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How can respositioning nucleosome affect gene expression?

Nucleosome respositioned to make promoter more accessible

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Compare active DNA with less active DNA (NUCLEOSOMES) how can you prove this?

Contains fewer nucleosomes More susceptible to digestion by DNase

Where are housekeeping genes and relatively rarely expression genes placed in relation to nucleosomes?

Housekeeping genes between Rarely expressed genes in between

Example of gene that can't be transcribed as DNA is bound to nuclear lamina

Hox genes

What does RNA polymerase required to associate with promoter sequence?

General transcription factor

What is transcription?

First of several steps of DNA based gene expression, in which a particular segment of DNA is copied into mRNA by the enzyme RNA polymerase

What do promoter regions signify?

Initiate transcription at the start of a gene

What is the role of GTFs?

Bind promoter sequences and create scaffold to recruit polymerase

Does RNA polymerase directly bind promoter?

What allows recruitment of specific polymerase to a given promoter?

Each promoter recognised by different subtype of GTF

How does eukaryotic gene expression show combinatorial control?

Many TFs work together to recruit proteins to form transcription complex and recruit RNA pol

In prokaroyitc DNA, what's the difference between the interaction between RNA pol and DNA?

RNA pol recognises the DNA itself, not the transcription apparatus

What initiates formation of initial basal transcription complex?

TATA binding protein binding to TATA box

What sort of DNA region is TATA box?

Cis regulatory element

What ensures correct and regulated gene expression in response to tissue specific and proliferation cues?

Activators and co activators/mediators binding outside core promoter elements

Describe what can influence gene expression outside of promoter region

Distal regulatory elements can decide if gene activated (trans)

How far away can distal regulatory elements be

1MB

What sort of regions are in distal regulatory elements?

Insulator Silencer Enhancer

Describe regulatory regions in eukaryotic DNA compared to prokaryotic

More complex

What is the different between cis and trans regulatory elements?

Cis-regulatory elements are often binding sites for trans-acting factors - they are present on the same molecule of DNA as the gene they regulate. Trans-regulatory elements can regulate genes distant from the gene from which they were transcribed.

What proteins bind to enhancer regions?

Activator proteins

What do activator protiens do?

Associate with the core promoter-TF complex to start transcription.

What is the role of a mediator?

Involved in the looping of chromatin, to allow interaction of regulatory elements with cis regulatory elements and GTFs

What interactions allow distal regulatory elements to affect gene expression?

Protein protein interactions folds DNA into loops allowing enhancer and promoter to interact activating transcription complex

What do enhancers do?

Stimulate transcription

What do silencers do?

Inhibit transcription (switch off promoter)

What does an insulator do?

Only activates promoter to right not left (i.e. limit how enhancer binds gene expression)

An example of a mechanism where extracellular control of gene expression

Hormones, diffuse into cells binding to receptor. Complex diffuses to nucleus and binds receptor elements in DNA that upregulate/down regulate gene expression

What do cis acting TFs do?

Bind promoter regions e.g. TATA box, GC box acting on gene immediately following promoter region

How else apart from transcription is gene expression controlled?

At levels of mRNA processing, translation and mRNA stability

What is the equivalent of TATA box in bacteria?

Pribnow box

What forms the transcription complex in prokaryotic cells?

Sigma factor and RNA pol

What are the 3 parts of promoter region?

Core promoter Proximal promoter Distal promoter

What does RNA polymerase do?

Synthesizes RNA from a DNA template. Initiates RNA transcription, Guides the nucleotides into position Facilitates attachment and elongation Has intrinsic proofreading and replacement capabilities Termination capability

What are properties of RNA polymerase?

Doesn't require primer so catalyses initiation and elongation of RNA Completely processive (single enzyme transcribes complete RNA) Proof reading mechanism

Where are the 3 isoforms of RNA pol found?

1 - nucleolus 2 - nucleoplasm 3 -nucleoplasm

What does RNA pol 1 produce?

rRNA

Does RNA pol require a primer?

What does RNA pol 2 produce?

mRNA, snNA, miRNA

Describe what happens in initiation?

Binding of TBP to TATA box, Sequential recruitment of TFIIB, TFIIA and TFIIF to promoter forming preintiitaiton complex. Complex recruits RNA pol 2, TFIIE and TFIIH. This initiation complex unwinds double helix

Describe normal rate of transcription activation by basal transcription activation?

Slow without activation factors

What happens in elongation?

In 5-3 direction No primer Normal base pairing U not T Nucleophilic attack by 3-OH at end of growing chain on alpha phos of incoming ribonucleoside triphosphate forming phosphodiester bond

What happens in protein independent termination?

Self complementary RNA palindromic GC rich region forms hairpin in RNA structure due to base pairing, hairpin followed by Oligo U sequence This destabilises association between RNA and DNA so they dissociate along with RNA pol 2 and double helix reforms

What does RNA pol 3 produce?

tRNA, some snRNAs

What RNA units join to form mRNA?

Ribonucleoside triphosphates

Nucleoside triphosphate vs nucleotide?

dNTP - base, sugar 3x phosphate NT - base, sugar, phosphate

During transcription, a complementary copy is made of..

The antisense strand (therefore copy of sense strand)