Module 11 Flashcards
gene regulation
The lowest level of chromosome organisation in a eukaryotic chromosome
nucleosome
A core nucleosome is composed of
two copies each of histone H2A, H2B, H3 and H4
An activator which positively regulates the expression of one or more genes
DNA-binding protein, transcription rates increase when an activator is bound to the DNA
Repressor proteins
Impede access of RNA polymerase to the promoter
The name of the major eukaryotic coactivator consisting of 20 or more polypeptides
mediator
When a regulatory protein represses transcription at specific promoters
Negative regulation
The role of an enhancer in eukaryotic gene transcription is to
Facilitate the expression of a given gene
What is underwound
lesser wound and it is strained
What happens when its underwound,
supercoil forms
What is type I topoisomerase purpose
Cut one strand and turn it to another side, phospahte bind to Tyr in the topoisomerase. covalent linkage, connected with no errors
What is type II topoisomerase
Holding two double stranded DNA, two monomer cutting the C gate and pass it through the other strand.
When does sister chromosome appear
metaphase
What does chromatin contain
1/3 DNA, 2/3 protein by mass
How many protein are in the histones
8
How many types are there in histones
5
Where is histone H1
outside, act as a clip to stabilise it
What are amino tails
from histones, allow the tail to interact with each other. binds to enzyme easier to modify and regulate them
Where does modification occur
histone tails and in the body of the histones
How is it modified
structure and packing of the chromatin
access to the DNA of DNA binding proteins
What does histone acetylation do
regulates chromatin condensation, wind by histones deacetylases and unwind by histone acetyl transferases HAT(decondensed chromatin)
What is chromatin remodlling
change section of chromatin for it to move around more. can remove histone, change histone variants, covalent modification of histones(by enzyme) change the accessibility of the DNA
How histone are read
scaffold protein, protein complex with catalytic activities and additional binding site to change the histones usage(modification.
What are the use of histone modification
Silencing genes, change expression, dna repair
When was chromatin more condensed
In mitosis
What are the stages of compaction
First level: when being transcript. 7 fold compaction
SEcond level: 30nm fibre, solenoid model, nucleosome are attach to one histone each, inaccessible DNA, cannot be transcripted.
What control the lose dna
chromosomal scaffold, loop 30nm fibre around the scaffold. may be transcript.
Are the grenes controlled?
yes
What can dna by transcript more easily
moving genes to another region, different nuclear neighbourhood. looped into an active region
What is one way to modify DNA
DNA methylation in eukaryotes(adding methyl group), it does not have effect of base pairing. when there is a CG dinucleotides. can be methylated on both strands
What is CpG islands
CpG change the way it interacts. a group of GC methylation. large sequences. Found in promoters to regulate transcription
Waht is one use of methylation
represses the expression of a gene
What is the use of DNA methyltransferases
to shutdown the expression of a gene
What happens when the new strand of the replicated ones dont not have CpG
maintenance DNa methyltransferases is used to methylate the new strand
What does epigenetic changes
no changes to DNA sequence
Are maintained in the cell but can by altered by signals.
Inherited from cell to cell
switches gene on or off
aceytlation in the histone tails and methylation of the cytosine
Does not change the bases
What direction does the outer ring of the E. coli genome go
Clockwise
What direction does the inner ring of the E. coli genome go
anti-clockwise
How are genes regulated
using UP element and other regions
Why must the genes be regulated
Does not have to express all the genes
What are transcription factors
elements(sequences in the gene), repress transcription or activates them.
How are bacterial genes being controlled together
operons( not in out genome)
How are operans operated
transcript multiple genes together as a unit
what is trp operon
to produce tryptophan,gaps are start and stop codons.
What happens when there is trp
cause repressor to active, block the transcription from making trp
what produces Lac repressor
LacI, made in a active state
What is Lac operon for
when there is no lactose, the active Lac repressor will stop Lac operons from producing
When there is lactose present, aldolactose will bind to the repressor, this will produce the gene.
What is B-galactosidase for
to form glucose as a energy source
What is the difference between trp operon and lac operon
With both have corepressor bound, trp will stop gene expression, while allolactose will express the gene. Both negative regulation
What does the operator sequence do
3 operators, palindrome.
How is Lac repressor bound
it binds as a dimer, work together as a tetremer. forms a loop, prevent polymerase to transcript
How many regulators are there for a single gene
multiple
How are gene activation like
synergistic, works together and does more transcription when lack of operon
Why is glucose a good energy source
does not take a lot of energy to breakdown compared to lactose. it will prioritise glucose first.
How does E. Coli use glucose first
when low glucose, there will be low ATP, cAMP increase, binds to CAP to activate it. binds to promoter of the lac operon to use lactose pathway. CAP overwrite lac operon
What are the 4 situations for cAMP production for prokaryote
When glucose high, cAMP is low, low level of gene expression when lactose is present. (no expression when lactose is absent)
When Glucose is low, cAMP high, high level of gene expression when Lac is present(none when lactose are not present)
How does cells change in the eukaryotic cell of the same DNA
difference in the regulation of the gene
What are the difference between eukaryotic and prokaryotic gene regulation
• Separation of transcription and translation
• Chromatin can block RNA polymerase access
• Basal transcription is low (eukaryote)
• Majority of regulation is positive, not negative
• There are more proteins involved in transcriptional regulation
• There are more transcription factors that control each gene
– on average 6 binding sites, but could be many more
- Combinatorial control
mostly are regulated in eukaryotic cell
What are the chromatin regulation
Methylation of DNA (prevent expression)
Histone acetylation ( allow transcription factors to bind and genes to expressed)
How eukaryotic transcriptional regulation work
+1 onwards are transcripted
regulatory element- DNA sequence that transcription factors bind to
Repressors bind to sequences called silencer
Activators find to sequence called enchancer or enhancer element
very regular
What is regulatory element
DNA sequence that transcription factors bind to
What is the use of an enhancer
it is where the activator is going to bind
How do you change the structure of the chromotin
Histone modification/ nucleosome remodelling complexes
What is the use of a mediator
It mediates between activators and the general transcription factor, facilitates binding of TBP, TFIIB. Makes transcription initiate.
What is the downstream of the gene
further region of the coding strand
Are shape of the dna constant
no
What is the major and minor groove
The large gaps and smaller gaps of the DNA, to bind to transcription factor.
What does the major grove do
DNA-binding protein will be able to bind to the DNA sequence without affecting the sequence
What are the features of eukaryotic transcription factors
- Transcription factors are usually made up of several domains
- There is only a small number of possible DNA binding domains
- Most Transcription Factors exist in large gene families
What is an example of a DNA binding domain
Helix-loop-Helix, it is a dimer(most do)
What is the use of Max
involved in cell growth and division
What can be formed in transcription factor
heterodimers(MYCMAX)
What is the use of the MYC MAX
involve in cell growth, activates, open chromatin for transcription
What is the use of MADMAX
repressed, not expressed, differentiation
What are the eukaryotic transcription factors like
Modular, members of the TF family can homo-dimerise or heterodimerise, control by the binding of many TF(combinarial control
How can there be so many protein produced
By alternative splicing, different protein produced from one gene
How does cell produce differennt mRNA
regulated for splicing repressor(harder for the splicing machinery from detecting)
Or Splicing activator to promote splicing
What is gene expression serparated into
1 Transcription initiation (how much)
2 post transcriptional precessing(how it is processed)
3 RNA stability (where does it go)
4 translational regulation (How it is translated)
5 Protein modification(how much is need to modify)
6 protein transport (where it is transported
7 Protein degradation (how long it should stay for)
How is transcription initiation regulated
by micro RNA (mi RNA)
where are mi RNA form
in the genes(multiple of them)
How is mi RNA formed
transported out to cytoplasm from nucleus, one will be removed.if mRNA is same as mi RNA, it will be broken down and destroy the RNA. If is it different, it will be repressed
What may be ask about a gene
- What cell types express gene1?
- Under what conditions do these cells express gene1?
- What can change or control the expression of gene1?
How to find whether a experiemtn is consistent
QRT-PCR
How is QRT-PCR done
extract RNA, get only mRNA, treat it with DNase, Run RT reaction, generate c-DNA. Run PCR, add it into a quantitative machine using light detection
How does QRT-PCR work
find the midpoint of the cycle graph. set a level and measure the number of cycle to reach the threshold. Or use a probe that base pair that are needed to be bind to, detect the florescent when the probe is bound.
