regulation of eukaryotic gene expression

Question 1

stages at which eukaryotic gene expression is regulated

Answer 1

1. transcriptional regulation
2. mRNA processing
3. regulation of mature mRNA
4. translation
5. post translation

Question 2

transcription in eukaryotes is same as prokaryotes =

Answer 2

each eukaryotic gene has promotor regions near the start of transcription - 5’ to transcription start site
- promotor sequences and regulatory promotor sequences bind to promotor by RNA polymerase

Question 3

eukaryotes - what does RNA pol I and III do

Answer 3

transcribes rrNAs, tRNAs, small nuclear RNAs

Question 4

eukaryotes - what does RNA pol II do

Answer 4

transcribes protein-coding genes and some noncoding RNAs

Question 5

what is a eukaryotic promotor

Answer 5

DNA sequence that allows initiation and regulation of transcription
-upstream (5’) of transcribed sequence

Question 6

what does core promotor of eukaryotic promoter contain

Answer 6

binding site for RNA pol II and general transcription factors
-sequences direct RNA pol II to start of transcription

Question 7

what does regulatory region (proximal control elements) of eukaryotic promoter contain

Answer 7

DNA sequences recognised by regulatory transcription factors - proteins that regulate whether transcription is initiated

Question 8

what do transcription factors do

Answer 8

bind to eukaryotic promoters, positioning RNA polymerase at the promoter
-helps to separate DNA strands to allow transcription to start
-allows RNA polymerase to leave promoter as transcription starts
-forms a pre-initiation complex needed for transcription to start

Question 9

what is TATA binding protein (TBP)

Answer 9

general transcription factor
-binds to DNA in minor groove and bends it, so RNA pol can bind to promoter

Question 10

what transcription factors needed to activate basal level of transcription

Answer 10

CBP and SP1

Question 11

do transcription factors have the same or different DNA binding domains

Answer 11

different

Question 12

transcription factors bind to DNA by specific

Answer 12

amino acid side chain : base interactions

Question 13

what are enhancers

Answer 13

direct bending of DNA and control timing and location of gene transcription
-enhancer sequences about 200 bp long
-can be close to transcription start site or positioned up to 50 kb from start site
-can be positioned upstream or downstream of promoter
-has multiple binding sites for transcription factors

Question 14

mediator:

Answer 14

complex of proteins that links upstream bound transcription factors to the basal complex

Question 15

3 regulatory DNA sequences regulate eukaryotic gene transcription

Answer 15

-core promoter region - has TATA box and sequences next to transcription start site
-upstream is proximal control region (regulatory region) that binds regulatory transcription factors
-enhancer sequences which bind regulatory proteins which interact with proteins at the promotor

Question 16

3 regulatory DNA sequences have cis regulatory sequences - what is this

Answer 16

bound by transcription factors to regulate transcription of genes on the same chromosome as the sequences

Question 17

3 regulatory DNA sequences have trans regulatory proteins - what is this

Answer 17

RNA pol II and transcription factors bind the trans regulatory proteins, which can bind to their target sequences on any chromosome

Question 18

how are eukaryotic promotors complex

Answer 18

can have multiple transcription start sites to allow multiple different transcripts to be generated from a single gene

Question 19

example of tissue specific transcription factors binding to promotor and enchancer sequences leading to tissue specific gene expression

Answer 19

transcription factor MyoD is specific to developing muscle cells
- MyoD binds to E box sequences in the promoters ad enhancers of muscle specific genes
- muscle specific gene expression is activated by MyoD, e.g muscle actin, creatine kinase

Question 20

cAMP in transcription

Answer 20

many genes in mammals are transcriptionally activated by cAMP
- example of cAMP-responsive gene = PEP carboxykinase catalyses oxaloacetate –> PEP formation in gluconeogenesis

Question 21

what are histones

Answer 21

small DNA binding proteins coiled around DNA to allow DNA to pack into chromosomes
-high proportion of basic amino acids - lysine and arg
-5 diff histone proteins

Question 22

histones direct packaging of DNA into nucleosome - what is this

Answer 22

basic subunit of chromatin
-nucleosome (chromatin fibres) form loops which are packed together to form a chromosome

Question 23

looser packing of chromatin and chromatin remodelling allows

Answer 23

transcription factors to access and bind to DNA

Question 24

what are open promotors

Answer 24

promotors of constitutively expressed genes (genes expressed in all cells) that are not packed into nucleosomes
- within nucleosome depleted regions (NDR)
- bound by activator proteins (ACT) to allow access for general transcription factors to activate transcription

Question 25

what are covered promotors

Answer 25

promotors of regulated genes that are packed into nucleosomes
-transcription only happens if the nucleosomes are loosened, displaced or removed
-activator proteins (ACT) and chromatin re-modelling proteins allow unpacking of the chromatin
-allows RNA pol II and transcription factors to bind and activate transcription

Question 26

chromatin modification by histone acetylation

Answer 26

addition of acetyl groups to specific lysines in the histones reduces +charge so histones bind DNA less tightly
-so loosening of chromatin - RNA pol II and transcription factors to bind DNA
-reversible

Question 27

how does DNA methylation influence transcription

Answer 27

methylation of cytosine at 5C position to form 5-methylcytosine
-inhibit transcription
-reversible

Question 28

how many histone proteins are found in a nucleosome

Answer 28

8

Question 29

sequences useful to search for when looking for protein coding sequences in a genome (3)

Answer 29

poly A addition site
TATA box
CAT box