Eukaryotic gene regulation

Question 1

how is transcription initiated

Answer 1

transcription factors and RNA polymerase bind to promoter region upstream from a gene

Question 2

chromosome puff

Answer 2

visible expanded region on a chromosome where active transcription occurs

Question 3

heterochromatin

Answer 3

densely packed
genes silenced

Question 4

euchromatin

Answer 4

loosely packed

Question 5

chromatin remodelling complexes

Answer 5

reposition nucleosomes allowing
transcription factors and RNA
polymerase to bind to promoters
and initiate transcription.
Uses energy from ATP

Question 6

histone modification concepts

Answer 6

Chromatin contains +ve lysine
and arginine amino acid
residues that electrostatically bind to negatively charged phosphate group on dna backbone
acetylation of amino acids alters charge on histone proteins to alter ability to bind to dna

acetyltransferases, deacteylases, methyltransferases etc

Question 7

histone acetyltransferases

Answer 7

add acetyl groups (from acetyl-CoA) to the lysine residues on histone proteins, neutralising the positive charge that attracts the DNA to the nucleosome

Question 8

histone deacetylases

Answer 8

remove acetyl groups
restore charge
blocks transcription

Question 9

effects of histone acetyltransferases on transcription

Answer 9

structural changes to chromatin, leading to chromatin relaxation. Heterochromatin to
Euchromatin. Recognition site for
transcriptional activator-more open

Question 10

DNA methylation

Answer 10

addition of methyl groups to cytosines
5-methylcytosine
recruits histone-modifying proteins to stabilise the chromatin
heritable
blocks TFs

Question 11

CpG islands

Answer 11

clusters of adjacent CG nucleotides near promoter

Question 12

genomic imprinting

Answer 12

form of gene expression where only one allele, either maternal or paternal, is expressed (other is silenced)
imprinted genes are passed down
regulated by epigenetuc modifications

Question 13

genomic imprinting with pregnancy
IGF2 and H19

Answer 13

IGF2 paternally expressed and promotes fetal growth
H19 maternally expressed, limits excessive growth/removal of resources from mother

Question 14

mechanism of x chromosome inactivation

Answer 14

Xist RNA binds to XIC (X chromosome inactivation centre). Xist RNA coats chromosome which triggers methylation and modifications that reduce transcription
Prevents overexpression of genes in females

Question 15

Xist gene

Answer 15

codes for RNA that is transcribed and undergoes splicing but does not code for a protein
recruits factors promoting methylation of DNA and histone modification

Question 16

core promoter

Answer 16

specific DNA sequence that RNA
polymerase and transcription
factors recognise
Contains TATA box

Question 17

regulatory promoter

Answer 17

upstream from core promoter
TF binding site
forms transcription initiation complex

Question 18

basal transcription apparatus

Answer 18

TATA
general TFs
RNA polymerase

Question 19

transcription factors (structure)

Answer 19

contain one or more DNA binding motifs that bind to DNA

Question 20

TFs in prokaryotes and eukaryotes

Answer 20

helix-turn-helix
alpha helices fit into major groove of DNA

Question 21

TFs in eukaryotes only

Answer 21

zinc fingers
leucine zipper (main)

Question 22

specific transcription factors

Answer 22

can act as activators or repressors, either directly, or by binding cofactors

Question 23

enhancers

Answer 23

bind to activators (TFs)
can undergo DNA looping to get close to gene

Question 24

silencers

Answer 24

bind to repressors

Question 25

transcriptional synergy

Answer 25

multiple TF work together to increase level of gene expression, interact cooperatively Number of enhancer sequences affects amount of transcription

Question 26

insulators

Answer 26

blocks activity of an enhancer on a promoter only when it lies between the two help create regulatory neighbourhoods

Question 27

regulatory neighbourhoods

Answer 27

Chromatin loops where genes and their regulatory elements interact more frequently topologically associating domains Held together by CTCF protein that helps form the loops by binding insulators cohesin also involved Maintains genome structure and prevents unwanted interactions between genes

Question 28

TAD

Answer 28

enhancers can interact with promoters only in the same TAD

Question 29

pre-initiation complex

Answer 29

Large protein complex of RNA polymerase II, general TFs and coactivators General transcription factors and RNA polymerase assemble on core promoter

Question 30

assembly of pre initiation complex

Answer 30

TFIID (TF) binds to TATA box other TFs recruited RNA polymerase II recruited

Question 31

initiation of RNA synthesis

Answer 31

RNA polymerase II is phosphorylated by TFIIH, initiating transcription process RNA polymerase moves along strand TFIIH unwinds double helix