Topic 9

Question 1

What levels are eukaryotic genes regulated at?

Answer 1

transcriptional, processing and translational

Question 2

What are transcription factors similar to in bacteria?

Answer 2

activators and repressors

Question 3

What other means can genes be induced by in eukaryotes?

Answer 3

environmental factors, and signaling molecules

Question 4

What are some examples of transcription being activated by heat!

Answer 4

Heat shock protein gene
glia cell receptors

Question 5

What are some examples of genes that are induced by light?

Answer 5

RBC in plants and chlorophyll

Question 6

What hormones can regulate transcription?

Answer 6

insulin, growth hormone, cortisol and stress hormones

Question 7

What are the four domains found in tfs?

Answer 7

DNA binding domain, protein binding, protein mods of histones, and sensors

Question 8

Why are motifs in tfs important?

Answer 8

identify tfs at a molecular level, allow them to bind DNA and modulate RNApol activity directly or indirectly

Question 9

What are the motifs on the zinc finger tfs?

Answer 9

B sheet and an a-helix bridged by interactions with a zinc ion

Question 10

How do zinc fingers work?

Answer 10

three residues from each finger recognize sequence in DNA

Question 11

How do HtH domains work?

Answer 11

helix closest to C terminus binds DNA and other helices mediate protein-protein interactions

Question 12

How do leucine zipper containing tfs work?

Answer 12

dimers bring two basic domains together to associate with two DNA strands

Question 13

What is an example of a leucine zipper tf?

Answer 13

Fos and Jun-oncogenes

Question 14

How do helix loop helix tfs work?

Answer 14

helices mediate protein dimerization and basic regions around helices promote DNA association

Question 15

What are the two cis regulators in eukaryotic gene expression?

Answer 15

promoter proximal elements and enhancers

Question 16

What are promoter proximal elements?

Answer 16

precede the promoter of a eukaryotic gene and where general tfs bind

Question 17

What do enhancers do?

Answer 17

bind special tfs farther away from gene-often tissue specific

Question 18

Where are enhancers in drosophila?

Answer 18

5’ region and intron

Question 19

What are the trans regulators in eukaryotes?

Answer 19

basal tfs and specific tfs

Question 20

What else do enhancers do to facilitate transription?

Answer 20

bridge different regions of genome to transcription site to facilitate access of general tfs to the promoter region

Question 21

What are enhanceosomes?

Answer 21

large protein complex that acts synergistically to activate transcription

Question 22

What insulators/silencers?

Answer 22

DNA element that blocks the action of an enhancer-chnage region topology

Question 23

What is the Gal pathway in yeast?

Answer 23

metabolic pathway breaking down galactose into glucose

Question 24

What is Gal4?

Answer 24

transcriptional master regulator that targets most Gal genes for expression by binding UAS enhancer

Question 25

What are the two domains of Gal4

Answer 25

DNA binding domain which brings activation domain to promoter

Question 26

What turns off Gal4 and how?

Answer 26

Gal80-binds activation domain

Question 27

What is the mediator complex?

Answer 27

co-activator complex that promotes DNA activation that doesn't bind DNA or part of RNA pol

Question 28

How can siRNAs regulate gene expression?

Answer 28

interact with complementary mRNA and degrade it to stall translation therefore reduce expression

Question 29

How do RNAis get formed?

Answer 29

signal from dsRNA

Question 30

What does dicer do?

Answer 30

cleaves dsRNA into siRNAs or miRNAs

Question 31

What do siRNAs and miRNAs then associate with and why?

Answer 31

RISC-which degrades non complementary strand and then scans cytoplasm with guide strand for mRNA

Question 32

What causes the degradation of the produced mRNA?

Answer 32

Ago on RISC

Question 33

What can RNAi do in terms of phenotypes?

Answer 33

mimic the phenotype of a mutation often in lesser effects and it is non heritable

Question 34

What are histones?

Answer 34

proteins that compact DNA into chromatin

Question 35

What are nucleosomes?

Answer 35

basic structural unit of chromatin

Question 36

How do chromatin influence gene transcription on a macro level?

Answer 36

regions with high chromatin content tend to be silenced transcriptionally because they cant reach the machinery

Question 37

How do chromatin influence gene transcription on a gene level?

Answer 37

nucleosome can be rearranged and wrapped DNA exposed at a specific locus

Question 38

What are heterochromatin associated with?

Answer 38

histone methylation and closed chromatin

Question 39

What are euchromatin associated with?

Answer 39

histone acetylation and open chromatin

Question 40

What is position effect variegation?

Answer 40

expression of a gene depends on its position relative to the local chromatin status

Question 41

How is PEV caused?

Answer 41

genes changing locus or when heterochromatin changes its position

Question 42

How does nucleosome positioning on genes effect transcription?

Answer 42

nucleosomes on enhancer prevent transcription

Question 43

Why is the histone code important?

Answer 43

diff chromatin mods cause repression or activation of genes

Question 44

What is an example of a gene regulated by histones?

Answer 44

IFN-B

Question 45

How is IFN-B regulated?

Answer 45

writers are recruited by enhancesosome to acetylate and phosphorylate histone tails in promoter region, chromatin remodels

Question 46

How is IFN-B regulation turned off?

Answer 46

eraser proteins remove mods and readers leave locus