Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

GEN > expressing the genome > Flashcards

expressing the genome Flashcards

1
Q

what is gene expression?

A

process by which the info from a gene is used to synthesis a functional gene product which is either a protein or a functional RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are the 3 stages of gene expression? and what happens during each stages

A

initiation: basal transcription machinery assembles on the DNA at the promoter
elongation
termination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what are the 3 common features of most promoters?

A 
transcription start site 
TATA box
sequences bound by transcriptional regulators which includee:
upstream activating sequences (UASs)
enhancers 
upstream repressing sequences (URSs)
silencers
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are core promoters?

A

start site+TATA box

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is basal transcription machinery?

A

RNA polymerase II+5 multi-subunit general transcription factors (TFIIB, D, E, H) which assemble sequentially

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is a transcription factor?

A

sequence specific DNA binding proteins that bind at or close to te core promoter and influence the efficiency of transcription initiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is DNA helicase?

A

subunit of TFIIH that uses energyy from the hydrolysis of ATP to open up the DNA double helix allowing RNA polymerase II to have access to the template strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is transcriptome?

A

total complement of mRNA molecules (or “transcripts”) produced in a specific cell or the population of cells comprising a tissue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what enzymes allows chromatin to be accessible?

A

chromatin-modifying enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

where does DNA methylation occur?

A

occurs at the 5 carbon position of the cytosine ring resulting in 5-methylcytosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what does the methyl group after methylation do?

A

inhibits transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what is genomic imprinting?

A

form of epigenetic inheritance where DNA methylation ensures only one parental allele is expressed
when the paternal allele is expressed, the maternal copy is silenced and vice versa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are the key modifications on histones? what do they do?

A

acetylation of lysine 27 –>promotes gene transcription
methylation of lysine 27 –> suppresses transcription and results in large regions of inactive chromatin
methylation of lysine 9 –> Di- or Tri- methylation silences gene promoters and prevents transcription
methylation of lysine 4 –> active promoters and gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is chromatin folding’s role?

A

it plays a role in enhancing transcript

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what are the different chromatin folding?

A

chromosomal looping
topologically associating domains
chromosomal compartments
chromosomal territories

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what are the different methods to determine genomic architecture?

A

CHIP-Seq
chromosome conformation capture (3C)
the encyclopaedia of DNA elements (ENCODE)

17
Q

what is the regulome?

A

noncoding genomic regions that have significant elements for gene regulation
they include promoters, transcriptional regulatory sequences and regions of chromatin and histone modification which modulate the activity and expression of the protein-coding genes as well as other functions

18
Q

what are the different layers of hierarchical structure of chromatin?

A

heterochromatin/euchromatin –> A and B compartments –> TADs and chromatin loops

19
Q

what can be the result of the formation or disappearance of chromatin loops between enhancers and promoters?

A

gain or loss, respectively of enhancer function and can alter transcription factor binding in the genome and contribution to disease progression

20
Q

what can TAD boundary deletions do?

A

can induce rewiring of promoter enhancer interactions allowing enhancers from neighbouring domains to ectopically activate other genes causing aberrant gene expression and disease

21
Q

what can mis regulation of Wnt signalling result to?

A

various diseases including cancer

if no Wnt beta-catenin is phosphorylated and constitutively degraded

22
Q

what are DNA methyltransferases (DNMTs)?

A

family of enzymes that have an important role in the inheritance of epigenetic markers

23
Q

what does DNMT1 do?

A

DNMT1 maintains DNA methylation by identifying hemimethylated DNA (=CpG dinucleotides that are methylated on the original DNA strand but not the newly synthesised strand) and methylating the unmethylated cytosine at such sites

24
Q

what is DNA demethylation? what are the 2 mechanisms of DNA demethylation?

A

removal of methyl group from DNA
the two mechanisms of DNA demethylation are:
1. active: through an enzymatic process that removes or modifies the methyl groupp from 5-methyl cytosine. the ten-eleven translocation (TET) family of enzymes are involved in active demethylation
2. passive: takes place on newly synthesised DNA strands in the absence of DNA methylation maintenance

25
Q

what enzymes are responsible for de novo methylation?

A

DNMT3A/B

26
Q

what is cell differentiation?

A

transition of a cell from one cell type to another and it involves a switch from one pattern of gene expression to another

27
Q

what is a totipotent zygote?

A

a cell that can give rise to any type of cells

28
Q

during fertilisation and normal embryonic dev. is the DNA in maternal and paternal germ cells methylated or demethylated? what process allows for the expression of appropriate genes for dev and cell differenciation?

A

demethylated

de novo methylation

29
Q

how does the maternal and paternal epigenome of the germ cells become demethylated?

A

paternal epigenome –> rapidly undergoes genome wide active DNA demethylation and remains demethylated following multiple cell divisions
maternal epigenome –> undergoes gradual passive demethylation

30
Q

at what stag of embryonic dev does de novo methylation start?

A

at blastocyst stage

31
Q

what happens during cell differentiation?

A

each cell type acquires a unique DNA methylation pattern that is subsequently maintained during each cell division

32
Q

what is induced pluripotency?

A

laboratory process by which somatic cells can be converted into induced pluripotent stem cells (iPSCs) with features similar to embryonic stem cells

33
Q

how many transcription factors generate induced pluripotent stem cells? what are they?

A

4

OCT4, SOX2, KLF4 and MYC

34
Q

what is direct reprogramming?

A

conversion of fully differentiated cells to other cell types, bypassing an intermediate pluripotent stage

GEN (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions