Lecture 38

Question 1

How many genes do eukaryotes have?

Answer 1

21,000 genes

Question 2

What are regulatory proteins in eukaryotes?

Answer 2

transcription factors that bind to DNA and control rate of RNA Pol transcription

Question 3

What is true about TF’s and their expression?

Answer 3

they are expressed tissue-specifically and some respond to outside signals

Question 4

What are the core promoter regions in eukaryotes?

Answer 4

the initiator, TATA box, and downstream promoter

Question 5

What are the upstream promoter regions in eukaryotes?

Answer 5

CAAT box and the GC box, both regulatory elements

Question 6

What are some examples of eukaryotic promoters?

Answer 6

thymidine kinase and H2B

Question 7

What are enhancers?

Answer 7

activators

Question 8

What are silencers?

Answer 8

repressors

Question 9

What to enhancers and silencers do?

Answer 9

They can increase gene expression or inhibit transcription by 200x

Question 10

What is true about enhancers and silencers?

Answer 10

They have short control sequences that bind to TFs, are tissue specific, have great distances from promoter and different polarity

Question 11

How do TF’s influence transcription?

Question 12

How was TF influence on transcription found?

Answer 12

Studying yeast and it was found that at the vitro level a transcription complex worked at the basal level

Question 13

What is the function of mediator complexes?

Answer 13

to transmit signals from the transcription factors to the polymerase

Question 14

Wht do mediators function as?

Answer 14

transcriptional coactivators

Question 15

What do mediators do?

Answer 15

linking upstream regulatory sequences, such as enhancers, with RNA Pol II and general transcription factors at the promoter region

Question 16

What is required for a successful transcription by RNA Pol II?

Answer 16

mediator complex

Question 17

What do transcription factors respond to?

Answer 17

steroid hromone, cAMP transcription, cell signaling

Question 18

What affects accessibility of DNA to RNA Pol and TFs?

Answer 18

histones and chromatin also known as chromatin remodeling

Question 19

What is the purpose of chromatin remodeling?

Answer 19

expose the promoter region for the transcriptional process

Question 20

What makes up a nucleosome?

Answer 20

octamer histone core with DNA wrapped around it

Question 21

What are histones?

Answer 21

proteins that contain N and C terminal domains

Question 22

What is the N tail responsible for?

Answer 22

specific histone modifications and regulation of nucleosome activity takes place

Question 23

What is the histone fold domain responsible for?

Answer 23

where histones fold and interact with each other and mediation of the heterodimerization of histone pairs occurs

Question 24

How do histone folds and tails help DNA?

Answer 24

They help the DNA and interact with it to stabilize its bending

Question 25

What bonds are needed to stabilize DNA?

Answer 25

About 40 hydrogen bonds between histone(H3 and H4) and the DNA. All within the minor groove

Question 26

What do H2B and H3 tails do?

Answer 26

The tails help direct DNA in a left handed wrapping to store negative superhelicity.

Question 27

What allows DNA to be in a loose conformation?

Answer 27

Euchromatin but mostly acetylation on the histone tails

Question 28

What does loose conformation do?

Answer 28

It allows for active transcription because they are loose and exposed

Question 29

What does tight conformation do?

Answer 29

it is hard for transcription to happen because it is not open. Transcription is mostly inactive

Question 30

What brings in the acetyl groups?

Answer 30

The HATS

Question 31

What brings in the methyl groups?

Answer 31

The HDACS

Question 32

What happens during histone modifications?

Answer 32

They can change the function of chromatin structure

Question 33

What do bromodomains do?

Answer 33

Interact with acetylated lysine residues. Promotes transcription and loosen up

Question 34

What do chromodomains do?

Answer 34

Interact with methylated histones(espec. H3K4). Tightens DNA.

Question 35

Can eukaryotes methylate their DNA?

Answer 35

Yes. It is done through epigenetic control. It doesnt change the sequence or anything, just methyls the group.

Question 36

What is epigenetic inheritance?

Answer 36

When the methyl changes continue down and passed down

Question 37

What is genomic imprinting?

Answer 37

When methyl isnt passed down because they are de-methylated but the methyl pattern continues to show

Question 38

What does the Poly tail and cap do in eukaryotic stability?

Answer 38

It protects from degradation. So is the loop, it provides protection.

Question 39

What does RNAi do? What does it regulate?

Answer 39

They regulate translation and sometimes transcription

Question 40

What are the classes of RNAi?

Answer 40

small RNA(siRNA) and microRNA(miRNA)

Question 41

What does siRNA do?

Answer 41

cellular defense mechanism

Question 42

What do miRNA do?

Answer 42

Help in developmental regulation

Question 43

What transcribes pri-miRNA?

Answer 43

By RNA Pol 2 from endogenous gene

Question 44

What does pri-mRNA do?

Answer 44

The sequence allows them to fold back on themselves. Hairpin loops through base-pairing

Question 45

What trims pri-mRNA?

Answer 45

It is trimmed by ribonuclease, Drosha, to leave the hairpin loop (pre-miRNA)

Question 46

What does Dicer do?

Answer 46

Second ribonuclease, Dicer, cleaves off the loop and miRNAs into smaller sections (20 bps) and degrades one strand

Question 47

How is RNA interference used?

Answer 47

It is used as natural defense against RNA viruses. Also used for clinical treatment.