Eukaryotic Gene Regulation

Question 1

what is the 5’ flank of gene

Answer 1

5’ (upstream) to transcription start site, contains important regulatory elements

Question 2

true/false: Eukaryotic genomes are larger than prokaryotic genomes

Answer 2

true

Question 3

cis-acting elements

name them + brief desc + level of transcription

Answer 3

• promoters → adjacent to gene, include transcription initiation, TATA box, basal level of transcription
• enhancers → can be far from gene, amplify or repress basal level transcription

Question 4

difference between proximal promoter and enhancer

Answer 4

their position in genome
* promoter = -1000 to -100 bp upstream of TSS
* enhancer = can be kilobases up/downstream of TSS, or within gene itself

TSS = transcription start site

Question 5

exons

Answer 5

segments of gene that end up in mature transcript that reaches cytoplasm, include UTRs

Question 6

introns

Answer 6

segments of gene in primary transcript but not in mRNA

Question 7

5’ capping function

Answer 7

to protect against nucleases

Question 8

why do eukaryotes have more levels of regulation? (3)

Answer 8

they have chromatin & transcripts require more processing & transcripts are exported from nucleus to cytoplasm

Question 9

function of each type of RNA polymerase in eukaryotes

Answer 9

1. RNA pol I → transcribes rRNA genes
2. RNA pol II → transcribes all protein-coding genes (mRNAs) & microRNAs
3. RNA pol III → transcribes tRNA genes & some small regulatory RNAs

Question 10

processing that RNA pol II transcripts undergo to generate mature mRNA (4)

Answer 10

• RNA splicing (removes introns)
• add 5’ GTP cap (prevent RNA degradation)
• cleave 3’ end
• add 3’ polyA tail

Question 11

basal transcription factors

definition

Answer 11

assist binding of RNA poll II to promoters

Question 12

key components of basal factor complex (2)

Answer 12

• TBP (tata box binding protein)
• TAFs (tbp-associated factors)

Question 13

components of TIC (transcription initiation complex) (2)

Answer 13

RNA pol II + basal complex

Question 14

TFs (regulatory transcription factors)

definition

Answer 14

proteins that bind to DNA seqs within proximal promoter or enhancer to control rate of transcripition of a gene (activate/inhibit transcription)

Question 15

how do TFs regulate? (3)

Answer 15

• interact w TIC components
• modify chromatin struc to make TSS more/less accessible
• can be activators/respressors (sometimes both)

Question 16

two ways activators can increase transcription

Answer 16

1. promote binding of TIC components or stabilising TIC complex
2. recruit co-activators

co-activators → proteins that open chromatin & allow transcription

Question 17

two ways repressors can decrease transcription

Answer 17

1. recruit corepressors that directly prevent RNA pol II complex from binding
2. recruit corepressors that close chromatin

Question 18

what type of proteins are TFs

Answer 18

modular proteins

Question 19

what does a typical TF consist of?

name them + brief definition

Answer 19

• DNA binding domain → facilitates binding to specific DNA seq
• Activation/Repression domain → interacts w TIC components or co-activators/repressors
• Ligand-binding domain → some have (e.g. steroid receptors)

Question 20

DNA-binding domains of activator proteins (2)

Answer 20

• have α helices to interact w major groove of DNA
• 3 motifs: HLH, HTH, Zinc finger

HLH = helix-loop-helix, HTH = helix-turn-helix

Question 21

dimerisation domains

+ common dimerisation motif in euks

Answer 21

specialized for polypeptide-polypeptide interactions

leucine zippers

Question 22

the 3 levels TF activity can be controlled at

Answer 22

1. allosteric interaction w small molecules
2. post-translational modifications to TFs
3. transcription factor cascades

Question 23

combinatorial regulation (3)

how its made possible

Answer 23

made possible by:
* 1 gene regulated by many TFs
* 1 TF regulate many genes
* many co activators/repressors

Question 24

2 examples of reporter genes used in eukaryotes

Answer 24

• lacZ gene, blue colour when X-gal is used
• gene for GFP (green fluorescent protein)

Question 25

in vivo vs in vitro

Answer 25

vivo: whole orgs → stably integrate reporter gene in transgenic orgs (seeds, eggs)
vitro: cells in culture → transfect reporter gene into cells in culture (stable/transient)