ADL Lecture 4: 15

Question 1

Activator proteins

Answer 1

bind regulatory sequences to stimulate transcription

Question 2

repressor proteins

Answer 2

bind other sequences to hinder transcription

Question 3

What are the differences in gene regulation between eukaryotes/prokaryotes?

Answer 3

Eukaryotes:

• processes of transcription and translation are uncoupled
• many genes are alternatively spliced to yield dif. products
• genes are typically mono-cistronic
• gene regulated by separate/mult. promoters
• regulatory proteins are found in large complexes

Question 4

What are the five steps of Gene regulation in eukaryotes?

Answer 4

1. Transcriptional regulation
2. mRNA processing
3. . Regulation of mature mRNA
4. Translation
5. Post-transltion

Question 5

What are the five sub-stages of transcriptional regulation?

Answer 5

a. Reg. proteins + TFs bind to consensus DNA sequences (promoter region) to facilitate transcription.
b. more reg. DNA sequences (enhancers/silencers) bind reg. proteins to facilitate transcription of specific genes in each cell type.
c. open chromatin struc. favorable for transcription formed by protein action
d. Other promoters utilized in different cell types to produce different pre-mRNA molecules
e. Methylation of DNA inhibits transcription

Question 6

What are the four sub-stages of mRNA processing?

Answer 6

a. capping of 5’ end, polyA of 3’ end, & intron splicing modify pre-mRNA
b. Other capping/PolyA sites can be used in diff. cell types
c. Other splicing produces diff. mature mRNA molecules from some cell types
d. RNA editing modifies base sequences of mRNA

Question 7

What are the four sub-stages of Regulation of mature mRNA?

Answer 7

a. Translational regulatory proteins bind mature mRNA to delay translation initiation
b. RNA silencing by RNA interference blocks mature mRNA translation
c. Transport of mature mRNA to cytoplasm is regulated
d. Regulation of mRNA stability

Question 8

What is the sub-stage of translation?

Answer 8

making of mRNA delays or prevents translation

Question 9

What are the three sub-stages of Post-translation?

Answer 9

a. Polypeptides are processed and modified in Golgi body before transportation out of cell.
b. Reg. molecules bind to a Polypeptide to alter function
c. reg. protein stability

Question 10

Structural motif

Answer 10

The characteristic three dimensional structure of a protein, sometimes obtained from crystal structure data (most common elements of structural motifs are alpha helices and others that form function domains of proteins)

Question 11

functional domain

Answer 11

protein region with a specific function or interaction; allow recognition and binding of specific DNA sequences

Question 12

Helix-loop-helix

Answer 12

two alpha helices separated by loop in each polypeptide. 2 polypeptides join to form a DNA binding dimeric protein. 1 alpha helix from each dimer binds regulatory DNA

Question 13

Leucine Zipper

Answer 13

2 alpha helices, 1 containing mult. leucine amino acids. 2 polypeptides form functional dimeric protein. Leucine-containing helices fave one another and interdigitate to form the “zipper” + other helix of each polypeptide binds DNA

Question 14

Homeodomain

Answer 14

3 helices form single function polypeptide & longest helix interacts with regulatory DNA sequences

Question 15

Zinc finger

Answer 15

Protruding loops or “fingers” containing about 24 amino acids each contain a central molecule of zinc bound to 2 cysteine and 2 histidine amino acids. 2/3 zinc fingers form in each polypeptide & each finger interacts w/ regulatory DNA

Question 16

What are the three sets of regulatory DNA sequences involved in eukaryotic gene regulation?

Answer 16

1. core promoter region
2. various proximal elements
3. enhancer sequences

Question 17

Core promoter region

Answer 17

contains the TATA box; immediately adjacent to start of transcription; bind RNA polymerase II and assoc. TFs

Question 18

Various proximal elements

Answer 18

upstream of core promoter region; bind regulatory proteins

Question 19

enhancer sequences (enhancers)

Answer 19

bind regulatory proteins/interact with proteins bound to other promoter segments. Can be upstream/downstream or “in” genes they regulate and can be very far away

Question 20

cis-actiing regulatory sequences

Answer 20

Sequences to which proteins bind to regulate transcription of genes located on the same chromosome as the sequences

Question 21

Trans-acting regulatory proteins

Answer 21

Proteins that act in trans by binding to cis-acting reg. sequences and consequently regulating nearby genes, either by activating or repressing transcription. (often referred to as TFs)

Question 22

Enhanceosomes

Answer 22

at enhancers; mult. proteins form large complexes

Question 23

Enhanceosomes action

Answer 23

• direct DNA bending into loops that allow enhaceosome proteins to interact with RNA polymerase and TFs at core promoter and proximal promoter elements
• controls timing/location of gene transcription

Question 24

UAS

Answer 24

upstream activator sequence

Question 25

UAS: Galactose absent – result?

Answer 25

Gal4 bound to Gal 80 = no transcription

Question 26

UAS: Galactose present – result?

Answer 26

Gal 80 bound by Gal3; Gal4 binds to UASg = transcription occurs

Question 27

The default state in many genes in bacteria is …

Answer 27

“ON” unless turned off by repressor

Question 28

The default state in many genes in eukaryotes is …

Answer 28

“OFF” unless turned on by an activator

Question 29

Silencer sequence

Answer 29

(cis-acting sequences) Regulatory DNA sequences that can repress transcription of specific genes that may be located distantly from the sequence

Question 30

insulator sequences

Answer 30

-cis-acting sequences located between enhancers/promoters of genes that need to be protected from action of enhancers

Question 31

insulators

Answer 31

• ensure only target gene is regulated by enhancer

- allow formation of DNA loops that contain the enhancer/intended target promoters while excluding non-target genes

Question 32

1. Enhancer activity help …

2. Insulator sequences … and can …

Answer 32

1. initiate transcription

2. block enhancer action … redirect actively to another gene

Question 33

Can an enhancer activate a gene in preference over a nearby enhancer whose action is blocked?

Answer 33

yes ;)

Question 34

Multiple promoters

Answer 34

Mult. promoters in eukaryotes are active in different cell types; results in diff. primary transcripts that contain same protein-coding regions; leads to independent regulation of transcript in diff. tissues/diff. stages of development

Question 35

Combinational control

Answer 35

few genes can control many others

Question 36

Specific (or strategically) placed enhancers act as…

Answer 36

“switches” (turn transcription on/off)

Question 37

One gene can have ____ that are regulated ___.

Answer 37

two or more promoters … differently

Question 38

What can interact and/or be tissue specific?

Answer 38

enhancers/silencers

Question 39

What regulates eukaryotic transcription? (Hint: there are three mechanisms by which trans-acting proteins access target DNA sequences)

Answer 39

chromatin remodeling is the defining feature of eukaryotic DNA packing into chromatin…

Question 40

What are the three basic mechanisms by which trans-acting proteins access target DNA sequences?

Answer 40

1. reg. sequences not tightly bound by histones; reg. proteins can easily access DNA sequences
2. Chromatin remodelers: change distribution/composition of histones
3. chromatin modifiers: enzymatically modify histones by +/- acetyl/methyl groups to particular lysine residues.

Question 41

Chromatin remodelers and chromatin modifiers mediate ___ transition from ___, heterochromatic DNA to ___, euchromatic DNA

Answer 41

reversible
inactive
active