Lecture 14

Front 1

Regulation of gene transcription / expression in eukaryotes is complex. Unlike bacteria regulatory sequences which are found in close proximity to promoter, human regulatory sequences can be located up to ___________ bp from the start site.

Back 1

50,000

Front 2

What are the two domains of the Gal 4 transcription factor?

Back 2

activation domain, and DNA binding domain

Front 3

Coming together of ___ Gal4 proteins leads to transcription. (homodimer)

Back 3

2

Front 4

How many binding sites for Gal4 upstream of the Gal1 gene?

Back 4

4

Front 5

These four biding sites for Gal4 form the _______________ (3) also known as UAS.

Back 5

Gal4 upstream activating sequence

Front 6

Gal1 genes are genes that encode for

Back 6

breakdown of galactose for energy

Front 7

The __________ regione of the Gal4 is needed to activate transcription.

This domain can activate transcription when fused with the DNA binding domain of ______.

Back 7

activating, LexA

Front 8

The DNA-binding domain of the eukaryotic _____________ resembles the bacterial _________________ domain.

Back 8

homeodomain, helix-turn-helix

Front 9

In the eukaryotic homeodomain, the 3rd alpha-helix makes contact with the __________ groove.

An arm off the 1st helix contacts the __________ groove.

The homeodomain binds DNA to repress transcription.

Back 9

major, minor

Front 10

Which two helixes of the homeo domain make up the helix-turn-helix motif?

Back 10

helices 2 and 3

Front 11

what amino residues make contact with the DNA in the yeast alpha2- transcriptional repressor?

Back 11

Ser, Arg, Arg, and Asn

Front 12

In the zinc finger domain, a zinc atom is bound by 2 ___ residues in an _______ helix and 2 ___ residues on a _________ sheet.

Back 12

His, alpha, Cys, beta

Front 13

The _________ helix binds the major groove of the DNA. ____ is required for DNA binding.

Back 13

Alpha, Zinc

Front 14

The ___________ sipper is composed of two long ________ helices. They both form the _____________ and DNA-binding domains.

DNA binding occurs in the _________ groove.

Back 14

leucine, alpha, dimerization


major

Front 15

The Yeast GCN4 PROTEIN is an example of a what kind of DNA binding motif?

Back 15

leucine zipper.

Front 16

Helix-loop-helix are found in eukaryotes. They are similiar to leucine zippers but a _______ seperates the alpha-helical _______________ and __________________ helices.
The alpha helix inserts into the _____________ groove of DNA and either activate or repressed transcription.

Back 16

loop, DNA binding, dimerization, major

Front 17

Activation domains are not well defined structures. The lack a ________ dimensional structure until it binds to something else.

Back 17

three

Front 18

Activation domains can be induced to form ________________ after binding to the transcriptional machinery.

Most common feature is the presence of ___________ amino acids.

They also contain important ____________ residues.

Also some activation domains include _________-rich (SP1) or _________-rich (CTF1) domains

Back 18

alpha helices, acidic, hydrophobic

glutamine, proline

Front 19

Binding of the activator to the enhancer can recruit the _______________ which in turn can recruit RNA polymerase II and _______ to the TATA box.

Back 19

mediator, TFIID

Front 20

Activation of transcription can be achieved by tethering the __________ to DNA.

Back 20

mediator

Front 21

Fusing a DNA binding domain, such as ______, to the ______ component of the ________ allows transcription at the corresponding DNA recognition sites for the binding domain.

Back 21

LexA, Gal11, mediator

Front 22

Activators can alter the structure of ___________.

Back 22

chromatin

Front 23

One activator bound to chromatin can recruit _________________ (3) and cause acetylation of histones. This opens up the chromatin and transcriptional machinery can then bind to promoters.

_____________ proteins recognize acetylated tails. An example is TFIID.

Back 23

histone acetyl-transferase


bromodomain

Front 24

Activators bound to chromatin can also recruit _______________ (3) which can remodel nucleosomes and expose promoters. Transcriptional machinery can then bind to promotors.

Back 24

chromatin remodeling complexes

Front 25

_________ block activation by enhancers.

They block enhancers from promoters only if it is physically between them.

Back 25

Insulators

Front 26

Regulation of the globin genes by the ______.

Globin genes are developmentally regulated. Only ___ is needed at a time.

Back 26

Locus control region (LCR), 1

Front 27

LCRs are made up of _________, ___________, and ____________-like elements.

Back 27

enhancer, insulator, promoter

Front 28

Which globin gene is always expressed?

Back 28

Alpha

Front 29

Human globin and mouse beta-globin genes are controlled by LCR while mouse HoxD genes are regulated by ___.

Back 29

GCR

Front 30

4 WAYS THAT BINDING OF A PROTEIN TO DNA CAN HELP ANOTHER PROTEIN BIND DNA:

a. _____________ formation
b. binding of 2 proteins to DNA allows recruitment of a _______.
c. first protein recruits _____________ remodeler which reveals a __________ site of a second protein.
d. binding of one protein _______ to a nucleosome allows binding of a second.

Back 30

heterodimer, third, nucleosome, binding, next

Front 31

Dual regulation of the HO gene in yeast:

_________ is only present in mother cells.

When SW15 binds to DNA, it recruits two things _______________ (3) and __________________ acetylase.

This opens and unpackages DNA.

_________ is only present at a certain stage of the cell cycle. It only binds when SW15 is bound.

OH gene is then expressed, which only happens at a certain stage of the cell cycle in mother yeast cells.

Back 31

SW15,

chromatin remodeling complex and histone aceylase

SBF

Front 32

The human beta-inerferon enhanceosome is 1 kb upstream of the _________ site.

With no bound factors the mRNA is in a _______ state so no transcription activators can bind.

Cooperative binding of the 3 activators: __________, ________, and __________ together with the archetectural protein _________ activates the beta-interferon gene. This structure together is called the ________________.

Back 32

start

bent

NF-kB, IRF, JUN-ATF, HMGA1, ENHANCEOSOME

Front 33

The enhanceosome recruits a transcriptional coactivator called _____ with ________-modifying properties.

Back 33

CBP, histone

Front 34

WHAT TYPE OF DNA BINDING DOMAINS DOMAIN DO EACH OF THESE HAVE?

JUN AND ATF -
IRF -
NF-kB

Back 34

leucine zipper

made up of 4 dif proteins

made up of 2 different proteins

Front 35

There is an evolutionary conservation in __________ sequence from mouse to human.

Back 35

enhancer

Front 36

combinatorial control of gene expression, that is ________ regulatory protein binding sites around eukaryotic promoters to allow for ______ control of expression.

Back 36

multiple, fine

Front 37

haploid yeast have 2 mating types, ___ and ___.

Back 37

a and alpha

Front 38

The a cell and the alpha cell each encodes cell-type-specific regulators: a cells make the regulatory protein ___, and alpha cells make the proteins ______ and _____.

A fourth regulatory protein, called _____, and is present in both cell types.

Back 38

a1, alpha 1, alpha 2

Mcm1

Front 39

In a cells, _______ activate a-specific genes. alpha specific genes are turned off how?

Back 39

Mcm1, nothing binds to the alpha specific genes so there is no activation

Front 40

in alpha cells, a specific genes are turned off by _______ and ________. Alpha genes are kept on by_________ and ________.

Back 40

Mcm1 and alpha 2

alpha 1 and mcm1

Front 41

in the a/alpha diploid cells, a specific genes are turned of by _______ and ______. alpha specific genes are turned off by __________. and haploid specific genes are turned off by _____ and _____.

Back 41

mcm1 and alpha2, nothing binding to them, alpha 2 and a1.

Front 42

What are the four ways in which eukaryotic repressors work?

Back 42

1. competition
2. inhibition
3. direct repression ( repressor protein binds mediator)
4. indirect repression

Front 43

How is indirect repression achieved?

Back 43

Through histone deacetylases, methylation, or nucleosome remodeling.

Front 44

Repression of the GAL1 gene in yeast:

The presence of glucomes allows _____ to bind the Tup1 repressor.

Tup1 recruits a ___________ (2) and also directly inhibits the transcriptional machinery at the promoter.

Back 44

Mig1

histone deacetylase

Front 45

What are the two signal transduction pathways?

Back 45

JAK/STAT AND Ras

Front 46

Explain the JAK/STAT PATHWAY:


_________ binds JAK receptor.
Causes JAK to ________ and phosphorylate itself through its kinase domain.
______ and ______ are recruited to the phosphorylation site and causes the protein to phosphorylate.
Phosphorylation causes the protein to ______ and travel to _________ and bind target DNA.

Back 46

cytokine
dimerize
SH2 / STAT
dimerize
the nucleus

Front 47

Explain the Ras pathway... which is highly conserved

_____ binds tyrosine kinase.
causes the receptor to _________ and phosphorylate itself and recruit protein ______ and ______.
These protein bind to phosphoryltion site on tyrosine kinase and activate ______-GDP to _____-GTP.

Back 47

signal growth molecule / (EGF)
dimerize
Grb2 and SOS
Ras, Ras

Front 48

Ras-GTP activates ___________ which activates __________ which activates __________ which activates a protein that enters the _________ and binds DNA to activate transcription.

Back 48

MAPKKK,
MAPKK
MAPK
NUCLEUS

Front 49

MAPK phosphorylates ___ to regulate interferon-beta.

Back 49

Jun

Front 50

In the absence of galactose, what binds Gal4 to inhibit its function to activate GAL1 genes?

Back 50

Gal80

Front 51

Silencing in the yeast telomere:

What binds the telomere?
This protein recruits ____ complexes. _______ deacetylates nearby nucleosome tails which bind _______ and ______ which bind more Sir2
to spread the silencing at the telomere.

Back 51

Rap1

Sir
Sir2
Sir3 and Sir4

Front 52

___________ of histone ______ prevents Sir2 binding to stop
the spread of silencing down the chromosome.

Back 52

Methylation, H3

Front 53

Influence of one chromatin modification on another:

_______ binds methylated-___ of histone H3 at the beggining of _______ to help condense chromosome. This prevents mitotic spindle attachment.

DURING METAPHASE A KINASE BECOMES ACTIVE TO PHOSPHORYLATE ____. This release ___ from the methylated _____ (histone tail) This allows the mitotic spindl to attatch to the chromosome,

Following the M phase, the phosphate is removed and Hp1 re associate on methylated ____

Back 53

HP1, K9, mitosis,

S10, HP1 k9,k9

Front 54

Switching a gene off is achived through DNA __________ and ___________ modification.

Back 54

methylation, histone

Front 55

Methylation block _________ binding and recruit DNA ___________ protein and ____________________ (2) complexes to insure no transcriptional activity occurs.

Back 55

activator, binding, chromatin remodeling

Front 56

What two mammalian genes are controlled by imprinting which is expression from just one of the two homologous chromosomes?

Back 56

igf2 and H19

Front 57

The imprinting control region (ICR) is an ____________.

It is bound by________ to inhibit expression of _________ but the __________ gene is expressed.

Methylation of the ICR region blocks __________ binding. Expression of ________ is inhibited but ________ gene is expressed by the downstream enhancer.

Back 57

insulator

CTCF, igf2, H19

ctcf, h19, ifg2

Front 58

the H19 gene is expressed only from the _______ chromosome, whereas Igf2 is expressed from the ________ chromosome.

Back 58

maternal, paternal

Front 59

The inheritance of gene expression patterns, in the absence of the initiating signal, is called ___________ regulation.

Back 59

epigenetic

Front 60

What are two examples of epigenetic inheritance.

Back 60

lysogenic state and DNA cystosine methylation.

These can be maintained through cell division.

Front 61

DNA cytosine methylation, can be maintained through cell divisions.

Methylated _____ sites are recognized on one strand and the corresponding _____ on the other strand is methylated to maintain the _____ state of DNA.

Back 61

CpG, CpG , parental