Gene Regulation

Question 1

Reverse transcriptase

Answer 1

Rna to DNA

Question 2

Functional RNA

Answer 2

Ribozymes, long non-coding RNAs, miRNAs

Question 3

Start codon of translation

Answer 3

ATG (DNA)

AUG (RNA)

Question 4

Stop codon

Answer 4

UAA, UAG, UGA (RNA)

TAA, TAG, TGA (DNA)

Question 5

Introns

Answer 5

Removed

Question 6

Cleae-polyadenylation site

Answer 6

Cut at the 3’ end and a bunch of A’s are added…defines end of last exon included

Question 7

Why is mRNA longer than protein?

Answer 7

5’ and 3’ UTR regions

Question 8

Enhancer/promoter location

Answer 8

Promoter - only at beginning

Enhancer - can be anywhere

Question 9

Upstream vs. downstream

Answer 9

Upstream - 5’

Downstream - 3’

Question 10

What controls expression of genes?

Answer 10

Trans-acting transcription factors and cis-acting DNA sites

Question 11

Cis

Answer 11

DNA motifs
Structurally linked to gene
Do not encode proteins but serve as docking sites for trans-acting genes

Question 12

Trans

Answer 12

Protein factors that regulate transcription of target genes…non covalentlybind to cis acting sites in a sequence specific manner

Question 13

Promoter

Answer 13

Adjacent to transcription start site…contains cis-acting site that assembles with RNA polymerase 2 complex…may interact with others

Question 14

Enhancer

Answer 14

Bind trans-acting transcription factors that positively influence chroomatin

Question 15

Silencer

Answer 15

Opposite of enhancer

Question 16

Trans-acting factor structure

Answer 16

Bipartite structure

Activation domain and DNA-binding domain

Question 17

Changes in amino acid sequence of trans-acting

Answer 17

Change affinity of binding to DNA

Question 18

Changes in nucleotides of cis-site

Answer 18

Increase or decrease affinity to protein

Question 19

Enhancers are a cluster of

Answer 19

Transcription factor binding sites

Question 20

Enhancers can

Answer 20

Alter chromatin or influence the recruitment of RNA poly 2 complex

Question 21

Enhancers are DNA elelments that are linked to

Answer 21

Increasing rate of transcription initation from a linked promoter

Question 22

Co-activator example

Answer 22

CBP/p300

HAT

Question 23

Co-activator

Answer 23

Interact with transcription factors (do NOT bind DNA)

Question 24

Co-activators may act as

Answer 24

Bridge between DNA binding proteins and Pol 2 transcription initiation complex

Question 25

Co-repressor example

Answer 25

HDAC

Question 26

Co-repressors

Answer 26

May block bridges between DNA binding proteins and Pol 2 transcription initiation complex

Question 27

Transcription facotrs can

Answer 27

Influence assempy of RNA polymerase 2 and associated factors on a promoter Influence rate of transcription initiation Interact with cis-acting site that are large distance away from promoters

Question 28

Combinatorial model of gene regulation

Answer 28

Interaction of multiple trans-acting transcription factors with multiple cis-acting binding sites will ultimately determine specificity, timing, and level of gene expression

Question 29

One TF can control

Answer 29

Multiple target genes

Question 30

Nuclear receptor superfamily of TFs conserved doamin

Answer 30

DNA-binding domain

Question 31

Generalized domain structure of nuclear receptors

Answer 31

Transactivation DNA binding (Zn) Ligand binding

Question 32

Orphan receptors

Answer 32

Nuclear receptors for which a ligand has not been ID'd

Question 33

Type 1 NR

Answer 33

In absence of ligand, in cytosol as a monomer with chaperone proteins...In presence of hormone, NR dissociates from chaperone, dimerizes, enters nucleus, binds to cis-acting sites of target genes and recruits co-activators and RNA polymerase to activate transcription

Question 34

Type 1 NR cis-binding

Answer 34

HRE - Hormone response element

Question 35

Type 2 NR

Answer 35

In absence of ligand, heterodimer bound to HRE and associated with co-repressors that repress...in presence of ligand, co-receptors dissociates, co-activators bind NR and recruits RNA polymerase to increase transcription Stays associated the whole time

Question 36

What do type 1 and 2 NR have in common?

Answer 36

Both do not require protein synthesis and are fialry rapid response

Question 37

HNF-4alpha

Answer 37

Hepatocyte nuclear factor 4alpha | Orphan receptor controls expression in liver, pancreas, and kidney

Question 38

Nuclear factor kB complexes

Answer 38

IKK - IKKgamma/NEMO, IKKalpha, IKKbeta NFKB - p50:relA heterodimer (others exist) IkB

Question 39

Nuclear factor kB pathway

Answer 39

Stimulus activates IKK complex IKK complex phosphorylates IkB Phosphorylated IkB is polyubiquitnated Polyubiquitanted IkB is degraded by 26s protesosome NFkB translocates to nucleus and binds cis acting site RNA pol 2 and associated factors recruited to promoter and transcribe gene

Question 40

Binding site of NFkB on DNA

Answer 40

NFkB RE

Question 41

NF-kB effect

Answer 41

Pro-survival | No proetin syntesis required

Question 42

Regulation of NF-kB

Answer 42

targets IkB...this provides feedback mechanism that can inhibit the NFkB complex