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H2 biology!!! > chapter 7: control of eukaryotic gene expression > Flashcards

chapter 7: control of eukaryotic gene expression Flashcards

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1
Q

what are the successive levels in which eukaryote DNA is packed into chromosomes?

A
  • the packing of DNA into chromosomes occurs via coiling and folding in successive levels
  1. linear DNA double helix
  2. 10nm nucleosome
  3. 30nm chromatin fibre/ solenoid
  4. 300 nm looped domains

chromosome!

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2
Q

how eukaryote DNA is packed into chromosomes: NUCLEOSOME

A

nucleosome is the most basic level of packing of DNA into chromosomes occurs eukaryotes

  • a nucleosome consists of negatively charged DNA wound around positively charged histone protein core
  • each core is also known as a histone o tamer as it contains 8 histone proteins
  • histone proteins have high proportion of positive charged amino acids (lysine and arginine), and they bind, and they bind tightly to negatively charged dna
  • the histone tails extend outwards from the nucleosome
  • adjacent nucleosomes are connected by linker DNA and H1 histone, to give the appearance of ‘ beads-on-a-string’
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3
Q

how eukaryote DNA is packed into chromosomes: 30nm chromatin fibre/ solenoid

A
  • interactions between histone tails, linker DNA and H1 histone
  • cause the string of nucleosomes to coil to form a chromatin fibre that is 30nm wide in diameter
  • which is a solenoid
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4
Q

how eukaryote DNA is packed in chromosomes: LOOPED DOMAINS

A
  • the 30nm chromatin fibre folds to form looped domains
  • that are attached to a base of scaffolding (non-histone) proteins
  • non histone proteins known as scaffold proteins are used to condense the solenoid to form looped domains
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5
Q

how is eukaryote DNA packed into chromosomes occurs eukaryotes: CHROMOSOMES

A
  • only during nuclear and cell division, the looped domains coil and fold further
  • compacting all the chromatin to highly condensed metaphase chromosomes
  • that can be seen under the light microscope
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6
Q

how is the packing in euchromatin different from the packing in heterochromatin?

A

euchromatin:
- loosely coiled/ less condensed/ less compact

heterochromatin:
- tightly coiled/ heavily condensed/ compact

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7
Q

compare how transcriptionally active euchromatin and heterochromatin are

A

euchromatin:
- transcriptionally active because RNA polymerase and general transcription factors are able to bind to promoter of genes

heterochromatin:
- transcriptionally inactive because RNA polymerase and general transcription factors are unable to bind to the promoter of genes
- packing of DNA into heterochromatin, where DNA is highly condensed is typically for the long term inactivation of genes
- where gene expression is repressed for a long period of time/ permanently

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8
Q

what are euchromatin and heterochromatin composed of?

A

euchromatin:
- 30nm fibres and looped domains

heterochromatin:
- 30nm fibres and looped domains and additional proteins that help in compaction

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9
Q

what happens during histone acetylation?

A
  • acetylation is the addition of acetyl groups to lysine in the histone tails
  • reaction is catalysed by histone acetyl transferase
  • when the lysine residues on histone tails are acetylated
  • their positive charges are neutralises
  • this causes fewer interaction of histone tails with the negatively charged phosphate groups of DNA that is being wrapped around the histones
  • and fewer interactions of histone tails with neighbouring nucleosomes
  • chromatin structure becomes less compact and condensed
  • RNA polymerase and transcription factors can bind to the promoters of genes in the acetylated region to form transcription initiation complex
  • allowing transcription to occur/ gene to be transcriptionally active
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10
Q

what does the deacetylation of histone tails cause?

A

deacetylation of histone tails by histone deacetylase causes:
- chromatin structure to become more compact and condensed
- RNA polymerase and transcription factors cannot bind to the promoters of genes in the deacetylated region
- transcription initiation com plex cannot form
- transcription is prevented/ gene is transcriptionally inactive

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11
Q

what happens during histone methylation?

A
  • methylation is the addition of methyl groups to lysine and arginine amino acid R groups in histone tails
  • this reaction is catalysed by histone methyltransferase

methylated histones can:
- attract proteins to bind to the histones
- causing DNA to wound tightly around the histones resulting in condensation of the chromatin
- RNA polymerase and transcription factors cannot bind to the promoters of of genes in the methylated region
- transcription initiation complex cannot form
- transcription is prevented/ gene is transcriptionally inactive

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12
Q

histone acetylation > ________
histone deacetylation > ________
histone methylation > ________
histone demethylation > ________
DNA methylation > ________

A

histone acetylation > allows transcription to occur
histone deacetylation > prevents transcription
histone methylation > prevents transcription
histone demethylation >allows transcription to occur
DNA methylation > prevents transcription

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13
Q

what happens when DNA methylation occurs?

A
  • DNA methylation is the addition of methyl groups to DNA
  • the reaction is catalysed by DNA methyltransferase

methylated DNA:
- attracts other proteins
- which in turn recruit histone deacetylases enzymes that remove acetyl groups from histone tails
- this makes the chromatin more compact and condensed
- RNA polymerase and transcription factors cannot bind to the promoters of genes in the methylated region
- transcription initiation complex cannot form
- transcription is prevented and gene is transcriptionally inactive

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14
Q

what are the 3 main groups of non-coding DNA in eukaryotes?

A
  1. control elements: regulatory DNA sequences that regulate level of gene expression
    - they include promoters, silencers and enhancers
  2. transcription factors: stretches of non-coding DNA that often disrupt coding sequences (exons) of eukaryotic genes
  3. repetitive DNA: DNA sequences which are present in multiple copies in the genome
    - eg. centromeres and telomeres
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15
Q

what are control elements?

A
  • they are regulatory DNA sequences that are non-coding
  • they serve as binding sites for RNA polymerase and transcription factors which are proteins that regulate transcription
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16
Q

CONTROL ELEMENTS
what is a promoter?

A
  • the site where transcription of a gene is initiated
  • a DNA sequence where RNA polymerase and general transcription factors bind to and initiate transcription
  • for eukaryotic genes, the promoter commonly contains the TATA box, with DNA sequence of 5’-TATAAA-3’
  • in eukaryotes, each gene is under the control of a single promoter
17
Q

CONTROL ELEMENTS:
what are enhancers/ silencers?

A
  • a DNA sequence where specific transcription factors bind to control the rate of transcription
  • enhancer: a control element that increases transcription rate
  • silencer: a control element that decreases / inhibit rate of transcription
  • these DNA sequences may lie far away from the promoter
  • however, they can still control the rate of transcription because the DNA can bend to bring the enhancer/ silencer close to the promoters of genes
  • these sequences are very important for tissue specific gene expressionf
18
Q

what are introns and exons?

A
  • sequences of DNA nucleotides in eukaryotic genes is usually not continuous, it is split into exons and introns
  • coding DNA segments in a gene are called extrons because they are eventually EXpressed
  • non-coding DNA segments in a gene are called introns because they are found between exons, hence INtervening the coding regions
19
Q

what is a poly-A-signal sequence?

A
  • it is a non coding sequence
  • a DNA sequence that is transcribed into an RNA sequence on the mRNA
  • this signals addition of poly-A-tail to the 3’ end of mRNA transcript during RNA processing
20
Q

what are transcription factors? and what are the two types of transcription factors?

A

transcriptional regulation in eukaryotes involves proteins called transcription factors that bind to:
- control elements
- and or other transcription factors/ RNA polymerase

  • to facilitate or inhibit the formation of transcription initiation complex on the promoter
  • the two types: general transcription factors and specific transcription factors
21
Q

what is the structure of a transcription factor?

A

transcription factors have two or more binding domains

  1. DNA binding domain is the region on the TF that binds to specific DNA sequences
    eg. promoter, enhancer, silencer
    the DNA binding domain is complementary in shape to the specific DNA sequence because:
    - different sequence of bases on DNA have different shapes
    - the major and minor grooves on DNA also have an effect on shape of that specific DNA
  2. protein binding/ activation domain is the region on the TF that binds to other transcription factors or proteins
    - for binding between different TFs to occur, the protein binding domain of one TF must be complementary in shape to the protein binding domain of another TF/ RNA polymerase
22
Q

describe the mechanism of the initiation of transcription at the promoter

A
  1. a general transcription factors have binds to the TATA box at the promoter
  2. binding of the general transcription factor recruits other additional general transcription factors and RNA polymerase to assemble at the promoter
    - forming the transcription initiation complex (which is relatively unstable at this point)
  3. this results in low rate of transcription
    - (Without additional regulatory factors (like enhancers or activators), transcription occurs at a basal or low level.)
23
Q

what does the formation of a transcription initiation complex ensure?

A
  • RNA polymerase is positioned correctly at promoter
  • DNA double helix is unwound and the DNA molecule is unzipped to expose the template DNA strand
24
Q

how do activators enhance the rate of transcription?

A

activators once bound to enhancers work by:
- accelerating and stabilising formation of transcription initiation complex
- modifying chromatin structure

25
Q

what is the mechanism of activators enhancing the rate of transcription?

A
  1. activators bind to enhancers
  2. a DNA bending protein binds to DNA, causing the DNA to bend to bring the bound activators close to the promoter
    - where RNA polymerase, general transcription factors and other proteins like mediator proteins are recruited to
  3. the activators bind to one or more basal transcriptionally factors and or mediator proteins and RNA polymerase, helping to accelerate and stabilise the formation of the transcription initiation complex on the promoter
    - highly increased rate of transcription of the gene
    - activators may recruit proteins and complexes such as histone acetyltransferase that loosens chromatin structure> which promotes the formation of TIC
26
Q

what happens when activators modifies chromatin structure?

A

some activators act indirectly by modifying chromatin structure

once bound, activators may recruit
- histone modification enzymes (eg. histone acetyl transferase)
- chromatin remodeling complexes
- histone chaperone proteins

  • this results in the chromatin structure to be loosened, allow RNA polymerase and general transcription factors to bind at the promoter
  • promoting the formation of the transcription initiation complex
27
Q

what are the four ways that can inhibit gene expression?

A
  1. competitive DNA binding
  2. masking of the activation domain on activator
  3. block assembly of transcription initiation complex
  4. modifying chromatin structure
28
Q

how does competitive DNA binding inhibit transcription?

A
  • enhancer and silencer DNA sequence overlap
  • activator and repressor proteins compete to bind to the same sequence of DNA
  • activators may be prevented from binding to enhancer sequence, preventing the transcription rate from being increased
29
Q

how does masking the activation domain on the activator inhibit transcription?

A
  • both repressor and activator bind to DNA
  • but the repressor also binds to the activation domain on the activator
  • this prevents activator from binding to and stabilising the transcriptional initiation complex, preventing the transcription rate from being increased
30
Q

how does blocking the assembly of transcription initiation complex inhibit transcription?

A
  • the repressor binds with some general transcription factors
  • this blocks the assembly of the transcription initiation complex on the promoter
31
Q

how does modifying the chromatin structure inhibit transcription?

A
  • once bound, repressions may recruit
  • chromatin remodeling complexes
  • histone deacetylases
  • histone methyltransferase
  • this results in the chromatin structure to e more compact
  • preventing RNA polymerase and general transcription factors from binding at the promoter
    and no transcription initiation complex is formed

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