Regulation of transcription

Question 1

What are cis acting sequences

Answer 1

• non protein coding regulatory sequences in DNA that are usually physcially close/connected to the sequences they regulate
• regulates genes by binding to regulatory proteins
• e.g. promoters

Question 2

What are trans acting sequences

Answer 2

• does not necessarily have to be close to the sequence that they regulate
• have to be expressed as regulatory proteins to regulate target sequence

Question 3

What is operator?

Answer 3

a cis acting sequnce where regulatory proteins bind

Question 4

what does negative regulation mean?

Answer 4

when DNA/protein interaction decrease transcription

Question 5

what does positive regulation mean?

Answer 5

when DNA/protein interaction increase transcription

Question 6

Genes can be repressible or inducible, what do they mean?

Answer 6

• repressible: transcription is ON by default
• inducible: transcription is OFF by default

Question 7

what is an activator protein?

Answer 7

regulatory protein that recruit RNAP to DNA

Question 8

what is a repressor protein

Answer 8

regulatory protein that inhibits RNAP binding or initiation

Question 9

What is a corepressor?

Answer 9

small molecule whose presence help reduce transcription through causing allosteric change in regulatory protein

Question 10

what is an inducer?

Answer 10

• small molecule whose presence help increase transcription through causing allosteric change in regulatory protein
• induces transcription

Question 11

what does positive repressible regulation mean?

Answer 11

• activator protein bound to DNA by default and activates transcription
• when corepressor binds activator, activator is prevented from binding the DNA => prevents transcription

Question 12

What does negative repressible regulation mean?

Answer 12

• Transcription is ON by default
• when corepressor binds repressor, repressor/corepressor complex binds DNA and prevents transcription

Question 13

What does positive inducible mean?

Answer 13

• transcription of is OFF by default
• when inducer binds to activator, activator activates trancription

Question 14

what does negative inducible mean

Answer 14

• Repressor protein bound to DNA by default and prevents transcription
• When inducer binds repressor ,repressor is prevented from binding DNA, and activates transcription

Question 15

what are transcription factors

Answer 15

• DNA binding proteins encoded by trans acting sequences
• can repress or activate transcription

Question 16

DNA sequences (cis acting sequences) bound by TFs can be high level assemblies or low level sequences, what are they?

Answer 16

• high level assemblies are cis acting regulatory DNA that is made up of many low level sequences
• low level sequences (response elements) are short sequences that are recognised by regulatory proteins (e.g. TFs). they are within high level assemblies
• e.g. promoter is a high level assembly that includes the low level sequence TATA box

Question 17

suggest some eukaryotic high level assemblies

Answer 17

• promoter
• enhancer
• silencer
• insulator

Question 18

suggest some eukaryotic low level sequences

Answer 18

• TATA box
• CAAT box
• BRE

Question 19

Suggest some prokaryotic high level assemblies

Answer 19

• promoter
• operator

Question 20

suggest a bacterial low level sequence

Answer 20

pribnow box (“TATAAT”)

Question 21

What is an operon?

Answer 21

a cluster of structural genes its adjacent regulatory sequences

Question 22

What do polycistronic and monocistronic mRNA mean?

Answer 22

• polycistronic mRNA: codes for more than one gene, common in prokaryotes
• monocistronic mRNA: codes for one gene, common in eukaryotes

Question 23

What is TRP operon

Answer 23

• the operon that codes for enzymes that catalyses tryptophan synthesis
• polycistronic

Question 24

what kind of regulation is TRP operon under?

Answer 24

negative repressible

Question 25

what is the repressor protein of TRP operon?

Answer 25

**TrpR**, coded for by regulatory gene *trpR* (gene name of a protein is italised and its first letter have to be lower case)

Question 26

what is the corespressor for TRP operon

Answer 26

tryptophan

Question 27

describe how TRP operon is turned OFF

Answer 27

* when tryptophan is abundant * a lot can bind to repressor, allosterically changing the TrpR =\> activating it * TrpR + tryptophan complex stops transcription by binding operator and blocking RNAP

Question 28

Describe when TRP operon is ON

Answer 28

* Not enough tryptophan available for TrpR to be in DNA-binding form * No TrpR + tryptophan blocking the operator, so RNAP can transcribe operon

Question 29

TRP operon is also regulated by attenuation, describe attenuation

Answer 29

* possible because **translation and transcription are concurrent** in bacteria * High [tRNA^trp]: * Ribosome reads through domain 1 easily & shields domain 2 * domain 3&4 form transcription terminator hairpin * Low [tRNA^trp]: * Ribosome stalls in 1 waiting for tRNA^trp * 2 binds 3 * 3&4 cannot form transcription terminator hairpin * RNAP can proceed transcribing the TRP operon * As a result: * when trp is abundant, trp synthesis is slowed * but when trp is not abundant, trp synthesis occurs as normal

Question 30

What is *trpL*

Answer 30

* a leader sequence: codes for the mRNA that will either form hairpin or not depending on the abundancy of tRNA^trp * translated but its peptide is degraded * role in fine tuning regulation of trp operon

Question 31

what is the lac operon

Answer 31

lac operon code for lactose degrading enzymes and lactose importer proteins

Question 32

how is the lac operon regulated?

Answer 32

**negative inducible**

Question 33

What is the repressor protein of lac operon

Answer 33

LacI

Question 34

what is the inducer of lac operon

Answer 34

lactose

Question 35

how is lac operon switched OFF?

Answer 35

* **LacI binds to operator**, loops the DNA * making DNA **inacessible to RNAP**

Question 36

how is lac operon switched ON?

Answer 36

* LacI **inactivated** by binding lactose * No LacI blocking the operator, so **RNAP can transcribe operon**

Question 37

lac operon is also under postive control by catabolite activator protein (CAP), how?

Answer 37

* When **[glucose] is low**, **[cAMP] will be high** * cAMP is the inducer that **binds to CAP** and allow it to **bind to CBS (CAP binding site)** of DNA * CAP/cAMP complex **actively recruits RNAP** * **transcription turns ON**

Question 38

What is the purpose of controlling lac operon with CAP?

Answer 38

* allows cells to **express preference** of what sugars to breakdown * cells **prefer glucose** over lactose * but when glucose is scarce, CAP allows cell to turn on lac operon =\> break down lactose

Question 39

(eukaryotes) what are enhancers?

Answer 39

* **cis acting** sequences * encodes regulatory sequences that **help recruit RNAP** * can be located near, within, upstream or downstream of a gene (sometimes by 1000s of nts away) * **binds transcription factors**

Question 40

what are silencers?

Answer 40

* cis acting sequence * when bind to transcription factors, **inhibits the transcription** of a gene

Question 41

regulatory proteins can be regulated by autologus regulation, how?

Answer 41

* some regulatory proteins can regulate themselves: **autologus** * **​**e.g. LacI inhibits the expression of its own gene *lacI* =\> when there's too much LacI, expresson of *lacI* is repressed

Question 42

transcription is also regulated by gene activation cascades, what is a gene activation cascade?

Answer 42

* where the activation or repression of a gene activates or repress a cascade of other genes * initiated by **external gradients or factors**